Leave a question! (new*)

Sometimes I get interesting questions that don’t quite fit into any of the existing topics already discussed within the blog and my obsessive/compulsive nature tells me that getting this questions in a random part/page/post of the blog doesn’t look quite neat either. Therefore I open this new page for all those questions you have! I don’t intend to have a repository like the one on the CCL, of course, but at least we could organize the info and make it readily available for those who might need it; in the end, that is what we do as scientists, right?

Please use tags at the begining of your comment, e.g.: #convergencefailure #visualization #gaussianerror or whatever you might think could help me, and others, to quickly find an answer to your queries. Feel free to reply to any comment you think you might have an answer to because the thing is, I don’t have all the answers (I wish I did, trust me). One other thing, try to summarize your questions in a coherent way and please do not post entire output files! I don’t have the time to check them in their entirety.

Well then, leave a question!

  1. Saman | July 8, 2011 at 2:42 AM

    Hello,
    I would be grateful if you could explain me the difference between the normal analysis done using HPmodes and without that. I want to compute the vibronic spectra of some dyes. I have used G09 to do that. However, the code is error prone! I got alot of error message without any documentation. Then, I shifted to source code, FCClasses to follow up. Now, I understood that I need normal mode analysis using HPmodes syntax to feed the code. I compared the outputs there is two series of normal analysis. I don’t clearly know how are the anlysi are done and what are the differences. For the first analysis after printing frequencies is like this:

    1 2 3 4 5
    A A A A A
    Frequencies — 50.1139 53.0576 78.4365 108.7226 132.2478
    Reduced masses — 5.1998 3.9481 5.5278 3.3061 1.5043
    Force constants — 0.0077 0.0065 0.0200 0.0230 0.0155
    IR Intensities — 0.3409 0.4114 0.5722 4.3762 1.4973
    Coord Atom Element:
    1 1 6 0.00006 0.00025 0.26758 0.00003 0.00017

    and the second analysis is like this :

    1 2 3
    A A A
    Frequencies — 50.1139 53.0576 78.4365
    Red. masses — 5.1998 3.9481 5.5278
    Frc consts — 0.0077 0.0065 0.0200
    IR Inten — 0.3409 0.4114 0.5722
    Atom AN X Y Z X Y Z X Y Z
    1 6 0.00 0.00 0.00 0.00 0.00 0.17 0.27 -0.05 0.00

    as far as I got, the G09 uses the second analysis while the FCClasses needs the first to perform the analysis. Any help would be appreciated.
    Saman

    Reply
    • joaquinbarroso | August 2, 2011 at 9:44 PM

      Hi Saman

      The HPmodes option only uses the high precision format (to five figures) vibrational frequency eigenvectors in the frequency output in addition to the normal three-figure output. So basically there is no difference, since it is using the whole set of numbers to do the math it only varies in the number of decimals used in the output.

      I hope this helps but if it doesn’t let me know, ok? Have a nice day!

      Reply
  2. JSA | July 17, 2011 at 6:28 AM

    Hi Sir,

    How can I make Gaussian print the first derivative of energy (dV/dx) for a given molecule in cartesian coordinates?

    Reply
    • joaquinbarroso | August 2, 2011 at 9:39 PM

      Hi!
      there must be an overlay (IOp) for that but unfortunately I don’t know it. Please contact Gaussian Tech support at their website. Do not worry about not having a license if that is the case, they will provide support for you even if you use a non-academic address.

      Sorry for not being too helpful this time. Thanks for reading!

      Reply
  3. harish | July 20, 2011 at 12:21 PM

    i am Harish jangra from the National Institute of Pharmaceutical Education and Reserach studing pharmacoinformatics. Sir, it will be my great pleasure to get your guidance, i am highly obliged and thankful if you suggest me about the basic algorithm behind Gaussian calculation (optimization)

    Reply
    • joaquinbarroso | August 2, 2011 at 9:34 PM

      Hi Harish!
      Wow, your question is not a short one! Basically Gaussian uses the Berny Optimization algorithm which calculates all forces on every atom (i.e. which way and how strongly is each atom being pushed or pulled by the rest of the atoms) then it also calculates the gradient of such forces and allows them to be pushed -or pulled- just a little bit and repeats the operation until the change in energy, forces and gradient, respect to the previous step is below a certain threshold.
      There are tons of papers about the original algorithm that you can find online.

      I hope this helps! Thanks for reading

      Reply
      • ninad | August 11, 2011 at 12:23 AM

        THANK YOU SO MUCH SIR FOR YOUR GENEROUS HELP.

  4. Hector | August 8, 2011 at 12:43 PM

    Hi,

    I’m currently a graduate student in an American University. I was wondering if you could comment on the opportunities in Mexico for computational chemists presently and how you see them developing in the future.

    Thanks,

    Hector

    Reply
    • joaquinbarroso | August 19, 2011 at 8:06 PM

      Hola Héctor,

      There are some oportunities for theoretical chemists in academia in Mexico but unfortunately not in the big universities, you’d have to look for a job in a smaller university or maybe at a private one which are right now trying to turn to research and not only teaching. The private industry could be another way to go although not many companies in Mexico do any research.
      I can’t speak as an authority on how the job market is moving for us comp chems, all I can do is give you this insight of mine and advice you to search search search within conacyt, universities all over the place, transnational companies, etc. Something good comes always up for people who is prepared for it.

      I hope you find something worth your while, in the meantime thanks for reading!

      Reply
  5. Vijay Kalamse | August 13, 2011 at 12:15 AM

    Dear sir,

    I am having a error while optimizing an structre in Gaussian 09. the error is as follows

    Berny optimization.
    Error in internal coordinate system.
    Error termination via Lnk1e in /home/software/g09-i7/g09/l103.

    Your suggestion is needed.

    Thank you

    Reply
    • joaquinbarroso | August 19, 2011 at 8:09 PM

      Hi Vijay,

      I think this means your structure is not well defined in terms of the internal coordinates. Check it with a visualizer and if possible use it to change the coordinate system from internal to cartesian. Also check if some atoms are too close to one another or if bonds are crossing paths.

      I hope this helps. Thanks for reading!

      Reply
      • vasavilatha | December 9, 2011 at 10:51 AM

        hi sir

        i am facing same problem i.e., error in internal coordinate system.but i very new to this computational chemistry i don’t know how to change the coordinate system from internal to Cartesian,and what do meant by bonds crossing paths..really i am running out of time.since one month kept on getting this problem when i try to optimize transition state to molecule on Gaussian 09. i am thankful if you suggest me any solution for this error .

        thank you

        hi vijay

        if you could have solved this problem based on sir suggestion,please why cant you help me to solve my problem.

        thank you

    • joaquinbarroso | December 20, 2011 at 10:57 PM

      Hello again Vijay

      Can you use gaussview? you have to click on “save cartesians” when you save the structure. Generate it with gaussview and then save it. That should fix it. Move all the atoms around until you eliminate all the bonds crossing each other.

      I hope this helps!

      Reply
  6. siddharth | August 20, 2011 at 2:27 PM

    hey do u know any free software available for chromatography ????then plz suggest me it s urgent plzzzzzz…………

    Reply
    • joaquinbarroso | October 18, 2011 at 12:52 PM

      Sorry but I’m not aware of any. Try the ACDLabs website.

      Reply
  7. Jo | August 23, 2011 at 2:47 PM

    Hi sir,
    Can you give me some ideas on spin-orbit coupling leading to the mixing of single and triplet states. Also can you mention the best program to calculate SOC. If you have already written about this please share me the link.

    Thanking
    Jo

    Reply
  8. Narges Mohamadi | September 1, 2011 at 10:20 PM

    Hi…would you please help me how to calculate the reduction potential using Gaussian?

    Reply
  9. Jyotsna Arora | September 10, 2011 at 5:49 AM

    Dear Sir,

    I am using G09 for metal ion studies and have tried giving different basis sets for the ligands and the metal ions.Both the moment I’ve used Gen or Pseudo keywords like shown below, the following errors are obtained.

    #RHF/GEN Pseudo=read
    comments…
    charge multiplicity
    molecular specifications
    C N 0
    6-31+G(d’)
    ****
    Hg 0
    LANL2DZ
    ****
    Hg 0
    LANL2DZ
    error : Wanted an integer as input
    Found a floating point number as input

    #B3LYP/GEN Opt Pseudo(SDD)

    #B3LYP/GEN Opt Pseudo(Read)
    Here I’ve specified the ECP basis set in the script but it still does not read the basis set.

    #B3LYP/6-31G Opt Pseudo(SDD)
    error : the heavy metal ion is not read by 6-31G basis set.

    Also the keyword pseudo=Read and pseudo=LanL2 with LanL2DZ with the heavy metal study the same?

    Reply
    • Bijan Mondal | February 8, 2012 at 5:18 AM

      Dear Jyotsna,
      Did you get any solution of your first error??
      Please share with me, I am having the same problem.

      Many thanks
      Bijan

      Reply
      • jyotsna arora | February 11, 2012 at 1:24 AM

        Dear Bijan,

        The problem is that when you are using different basis sets for different atoms esp. an ECP basis set then you have to specify the ECP basis set in the input file as

        C N 0
        6-31+G(d’)
        ****
        Hg 0
        LANL2DZ
        ****
        Hg 0
        (put the ECP basis set of the desired metal here)

        Hope this helps

        Regards
        Jyotsna

  10. nicola | September 14, 2011 at 6:38 AM

    Dear Sir,
    I’m interested to know if there is a software (better if it is free) that can create and plot Fukui functions from gaussian output.

    Thank you!

    Nick

    Reply
    • joaquinbarroso | November 18, 2011 at 9:57 PM

      I would suggest to use Molekel or Molden. As far as I know there isn’t a “button” to click on and get the plots so what you have to do is to substract the electronic density of the altered wavefunction (the one with a different Ne) from the one of your reference state (the one with the reference Ne). So, you have to generate both densities first and then you have to substract one from the other according to the equations found here
      http://joaquinbarroso.com/2010/07/26/how-to-calculate-fukui-indices/

      I hope this helps. Thanks for reading!

      Reply
  11. Minmin | September 19, 2011 at 2:51 PM

    Dear Sir,

    Now I use gaussian to calculate a cluster which made by 85 atoms, I make it two layers the higher layer is QM and lower layer is MM. Here is a problem comes, I cannot view the MO in the gaussview. As I see, the reason is the gaussian don’t calculate orbital for MM layer. Do you know any other ways to let it show MO for only QM layer?

    Here is my input file,

    #p opt=tight freq oniom(b3lyp/lanl2dz:uff) nosymm geom=connectivity scf=maxcycles=300 int=ultrafine

    pt4

    0 2 0 3 0 3
    Au- 0 3.558584 2.275638 -3.710549 L
    Au- 0 1.820176 2.360213 -1.802881 L
    Au- 0 0.153637 2.484202 0.005572 L
    Au- 0 -1.572773 2.561742 1.759631 L
    Au- 0 -3.392271 2.688492 3.587681 L
    Au- 0 -3.411779 0.208170 3.726424 L
    .
    .
    .

    Many Thanks!

    Minmin

    Reply
    • joaquinbarroso | December 20, 2011 at 9:33 PM

      Hi Minmin!

      I’m not sure this is possible with Gaussview and I’m not aware of any other software that could do it.
      Try to visualize them directly from a formatted chk file. It might work

      Hope this helps

      Reply
  12. Thorsten Jaskolla | September 20, 2011 at 11:34 AM

    Dear Sir,

    I try to calculate sodium cation affinities with MP2=Full. Geometry optimization for neutral and sodiated species using e.g.

    %chk=/home/j/neutral.chk
    %nproc=12
    %Mem=46GB
    #MaxDisk=1000GB
    #MP2=Full/6-311+G(2d,2p) Opt Test

    works fine with the Linux 64 Bit G09 (Revision A.02) version. However, all subsequent frequency calculations using optimized geometries crash. The Input-File is e.g.

    %RWF=/scratch/tmp/j/1,200GB,/scratch/tmp/j/2,200GB,/scratch/tmp/j/3,200GB,/scratch/tmp/j/4,200GB
    %chk=/home/j/sodiated.chk
    %nproc=12
    %Mem=46GB
    #MaxDisk=4000GB
    # freq rmp2=full/6-311+g(2d,2p) geom=connectivity test

    [No Title]

    1 1
    C -3.46469800 -0.12993500 -0.00003900
    C -3.12196400 1.22077200 0.00005500
    C -1.78463000 1.58038600 0.00014400
    C -0.77093400 0.60304900 0.00012400
    C -1.13980000 -0.75590900 0.00002700
    C -2.47539400 -1.11671900 -0.00005200
    Cl -5.12660400 -0.59284000 -0.00014700
    C 0.58398800 1.07838200 0.00019300
    C 1.75328900 0.38429100 0.00026000
    C 3.07273300 1.04229600 0.00048100
    C 1.89914400 -1.03108600 0.00019200
    O 4.12878100 0.41326000 -0.00007800
    N 2.22857600 -2.15703400 0.00018700
    O 3.02120100 2.36840300 -0.00043000
    H -3.89510400 1.97234700 0.00006100
    H -1.51424800 2.62675400 0.00021800
    H -0.39860800 -1.53873900 0.00000300
    H -2.76030400 -2.15684400 -0.00013200
    H 0.70057800 2.15472200 0.00027200
    H 3.92868400 2.70551800 -0.00095500
    Na 4.63463400 -1.82660900 -0.00023000

    1 2 1.5 6 1.5 7 1.0
    2 3 2.0 15 1.0
    3 4 1.5 16 1.0
    4 5 1.5 8 1.5
    5 6 2.0 17 1.0
    6 18 1.0
    7
    8 9 2.0 19 1.0
    9 10 1.0 11 1.5
    10 12 2.0 14 1.5
    11 13 3.0
    12
    13
    14 20 1.0
    15
    16
    17
    18
    19
    20
    21

    The calculation works for about 2 days and generates a combined scratch-file size of about 258 GB (splitted files). Without an error the calculations ends at the same point (just before the population analysis would start):

    Gaussian Output File:

    Entering Gaussian System, Link 0=/Applic.PALMA/gruppen/q0grimme/g09/g09
    Initial command:
    /Applic.PALMA/gruppen/q0grimme/g09/l1.exe /scratch/tmp/j.9544/Gau-9549.inp -scrdir=/scratch/tmp/j.9544/
    Entering Link 1 = /Applic.PALMA/gruppen/q0grimme/g09/l1.exe PID= 9550.
    ******************************************
    Gaussian 09: EM64L-G09RevA.02 11-Jun-2009
    19-Sep-2011
    ******************************************
    %RWF=/scratch/tmp/j/1,200GB,/scratch/tmp/j/2,200GB,/scratch/tmp/j/3,200GB,/scratch/tmp/j/4,200GB
    %chk=/home/j/sodiated.chk
    %nproc=12
    Will use up to 12 processors via shared memory.
    %Mem=46GB
    ———————————————————————-
    #MaxDisk=4000GB # freq rmp2=full/6-311+g(2d,2p) geom=connectivity test
    ———————————————————————-
    1/10=4,30=1,38=1,57=2/1,3;
    .
    .
    .
    .
    Inverted reduced A of dimension 497 with in-core refinement.
    End of Minotr Frequency-dependent properties file 721 does not exist.
    End of Minotr Frequency-dependent properties file 722 does not exist.
    MDV= 6174015488.
    Form MO integral derivatives with frozen-active canonical formalism.
    Discarding MO integrals.
    Reordered first order wavefunction length = 1153152288
    WUsed= 838072415 WInt= 6228120 WEnd= 13283563520
    Dk804= 4115560752. Dk1111= 0. Dk1112= 12923258400.
    MaxDsk=536870912000 LAFull= 1153152288 DskLim=536870912000.
    NUsed=29632743563.20077466863.14050795516.12680526328.10543911627. 9119501826.
    In DefCFB: NBatch= 1 ICI= 58 ICA=414 LFMax= 60
    Large arrays: LIAPS= 22894001280 LIARS= 3140649540 words.
    Semi-Direct transformation.
    ModeAB= 4 MOrb= 58 LenV= 6168992221
    LASXX= 2811761526 LTotXX= 2811761526 LenRXX= 5642084038
    LTotAB= 2830322512 MaxLAS= 2944453056 LenRXY= 0
    NonZer= 8453845564 LenScr= 16973996032 LnRSAI= 2944453056
    LnScr1= 5912000000 LExtra= 866684027 Total= 32339217153
    MaxDsk=536870912000 SrtSym= T ITran= 4
    JobTyp=0 Pass 1: I= 1 to 58.
    (rs|ai) integrals will be sorted in core.
    SymMOI: orbitals are not symmetric.
    Spin components of T(2) and E(2):
    alpha-alpha T2 = 0.1101843022D+00 E2= -0.3379652408D+00
    alpha-beta T2 = 0.5524282940D+00 E2= -0.1962767113D+01
    beta-beta T2 = 0.1101843022D+00 E2= -0.3379652408D+00
    ANorm= 0.1882974720D+01
    E2 = -0.2638697594D+01 EUMP2 = -0.12103953608513D+04
    IDoAtm=111111111111111111111
    Differentiating once with respect to electric field.
    with respect to dipole field.
    Differentiating once with respect to nuclear coordinates.
    There are 1 degrees of freedom in the 1st order CPHF. IDoFFX=0.
    LinEq1: Iter= 0 NonCon= 1 RMS=2.81D-03 Max=1.47D-01
    LinEq1: Iter= 1 NonCon= 1 RMS=7.99D-04 Max=1.87D-02
    LinEq1: Iter= 2 NonCon= 1 RMS=3.70D-04 Max=1.80D-02
    LinEq1: Iter= 3 NonCon= 1 RMS=2.02D-04 Max=9.45D-03
    LinEq1: Iter= 4 NonCon= 1 RMS=8.56D-05 Max=4.10D-03
    LinEq1: Iter= 5 NonCon= 1 RMS=4.33D-05 Max=3.30D-03
    LinEq1: Iter= 6 NonCon= 1 RMS=1.53D-05 Max=5.51D-04
    LinEq1: Iter= 7 NonCon= 1 RMS=6.04D-06 Max=2.60D-04
    LinEq1: Iter= 8 NonCon= 1 RMS=2.19D-06 Max=5.37D-05
    LinEq1: Iter= 9 NonCon= 1 RMS=7.24D-07 Max=2.39D-05
    LinEq1: Iter= 10 NonCon= 1 RMS=2.61D-07 Max=9.41D-06
    LinEq1: Iter= 11 NonCon= 1 RMS=1.05D-07 Max=4.89D-06
    LinEq1: Iter= 12 NonCon= 1 RMS=5.11D-08 Max=2.64D-06
    LinEq1: Iter= 13 NonCon= 1 RMS=1.81D-08 Max=7.44D-07
    LinEq1: Iter= 14 NonCon= 1 RMS=5.33D-09 Max=1.51D-07
    LinEq1: Iter= 15 NonCon= 1 RMS=1.97D-09 Max=6.96D-08
    LinEq1: Iter= 16 NonCon= 1 RMS=7.09D-10 Max=2.36D-08
    LinEq1: Iter= 17 NonCon= 1 RMS=2.14D-10 Max=5.42D-09
    LinEq1: Iter= 18 NonCon= 1 RMS=6.35D-11 Max=2.21D-09
    LinEq1: Iter= 19 NonCon= 1 RMS=2.25D-11 Max=1.02D-09
    LinEq1: Iter= 20 NonCon= 0 RMS=8.24D-12 Max=4.12D-10
    Linear equations converged to 1.000D-10 1.000D-09 after 20 iterations.
    End of Minotr Frequency-dependent properties file 721 does not exist.
    End of Minotr Frequency-dependent properties file 722 does not exist.
    Symmetrizing basis deriv contribution to polar:
    IMax=3 JMax=2 DiffMx= 0.00D+00
    G2DrvN: will do 22 centers at a time, making 1 passes doing MaxLOS=2.
    Calling FoFCou, ICntrl= 3107 FMM=F I1Cent= 0 AccDes= 0.00D+00.
    FoFDir/FoFCou used for L=0 through L=2.
    End of G2Drv Frequency-dependent properties file 721 does not exist.
    End of G2Drv Frequency-dependent properties file 722 does not exist.

    Do you have any explanation for this error?

    Sincerely,

    T. Jaskolla

    Reply
    • joaquinbarroso | December 20, 2011 at 9:26 PM

      Hello T.

      I haven’t seen this error before. Are you performing the second set of calculations on the same machine?
      Try using density=current

      Hope this helps!

      Reply
  13. Meenakshi | September 22, 2011 at 5:30 AM

    Dear sir,
    My molecule name is 2-Chloro alpha alpha alpha trifluoro 3,5-dinitrotoluene. While submitting this molecule for frequency calculation, it is saying that there is ” Input conversion error in IntKMC” . I don’t know how to eliminate that error .and seeking your assistance to continue my work.

    Reply
    • joaquinbarroso | October 18, 2011 at 1:11 PM

      Hello Meenakshi

      Haven’t seen this error before but there seems to be something wrong with the input. Try redefining the molecule specification section. Did you pre-optimized the structure? Are you reading it from another program?
      I think I need more information to help you, ok?

      I hope I can help you in the near future.

      Reply
  14. Agapito Serrato III | October 8, 2011 at 12:44 PM

    Dr. Barroso,

    In a reponse to someone trying to visualize a hypersurface of a scan you suggest using “Origin, GNUplot or in the worst case scenario with MS Excel”. What other programs would you suggest a S.T.E.M. student should be familiar with before entering grad school? Excluding, the basic Microsoft suite of programs like word, ppt, and excel.

    Thank you,
    Agapito

    Reply
    • joaquinbarroso | October 18, 2011 at 1:06 PM

      Hello Agapito, my friend who I still haven’t met!

      I would suggest learning how to work with software for statistical analysis such as Origin or other commercial packages with the same purpose.
      Learning your way around Unix/Linux/etc. is important since you will have the need for more powerful computing capabilities which are best provided by these systems.
      Coding is a very valuable skill these days, although you don’t have to be exactly an expert on programming, just knowing your way around a certain language will help you understand and modify existing codes (almost nobody codes from scratch anymore, the closest thing still involves taking published subroutines for tasks such as integrating). Suggested languages to learn: C and its variants, Python and Fortran if available (in that order of priority).
      MATLAB can also be a great asset to your skills.

      From the top of my head I think this is the most important I can think of right now for any generic STEM grad student but if I think of something else I’ll get back to this comment.

      How about those Rangers? Texans are pretty excited, I guess. I’m betting on them to win the World Series, despite the fact I was secretly rooting for the Tigers.

      Have a nice day!

      Reply
  15. brady | October 19, 2011 at 10:44 AM

    Dr. Barroso,

    Wow this is a great Gaussian site, and you are so helpful and prompt with all levels of questions. if you don’t mind, I have two totally basic ones, and would really appreciate your help. I’m using 09, and have Gauss-View. : )

    1st involves the Gen keyword and a .gbs file. When “downloading” a basis set from the EMSL, is it just copy-paste the desired atoms from the pop-up window (from the desired set) and save as a .gbs in your directory? Basically how does downloading basis sets from the EMSL work if Gaussian needs a .gbs file?

    2nd involves Using NBO analysis in a TD excited states calculation. I know where the bond population and energy are for “natural” orbitals in the analysis. How/where do I assign calculated UV-vis peaks to their natural orbital excited transitions? Thanks so much!

    Reply
    • brady | October 31, 2011 at 9:59 AM

      Dr. Joaquin,

      Scratch the NBO TD analysis. I’ve been able to parse the .log files to assign population density types to transitions by coefficients etc. As I believe you’ve commented on, NBO & DFT do not really mix in GaussView (using 5). So I’ll only be using NBO for bond energy (kcal) for certain donor interactions in the .log.

      However, If you have any advise on the Gen keyword related to installing basis sets from the EMSL, your help would be truly appreciated.
      -b

      Reply
      • joaquinbarroso | November 18, 2011 at 9:17 PM

        Hi Brady

        First of all please forgive the lateness of my response (sheesh! this has become a usual opening line in my replies; I either reply sooner or create a shortcut so I don’t have to type it all every time!)
        About the GEN keyword, please defer to my latest post which can be seen here

        http://joaquinbarroso.com/2011/11/02/gen-keyword-gaussian/

        It is sometimes confusing what to do with the EMSL basis sets but I hope this post helps you.

        Best wishes and thanks for reading!

    • Bijan Mondal | February 17, 2012 at 1:35 AM

      Dear Brady,

      Please share how you solve your problems regarding gen keyword and EMSL basis set, and how you assigned uv-vis peaks to their natural orbital exited transition in a TD calculation?

      Many thanks

      With best regards,
      Bijan Mondal

      Reply
      • joaquinbarroso | February 17, 2012 at 9:13 AM

        In this blog there is a post about the use of the GEN keyword. Try searching it with the search field at the left side of the page

  16. M J Alam | October 24, 2011 at 10:19 PM

    Hello Sir,
    Let me know about PBC calculations in Gauassian. Is it calculations in solid phase? Is it possible to do calculations in solid state with Gaussian?

    Thank-you

    Reply
    • joaquinbarroso | November 18, 2011 at 9:25 PM

      Hello Alam!

      PBC would be a great post for the near future! Thanks for the idea :)
      Now, to answer your question. PBC generates a periodic model from a small set of atomic coordinates based on symmetry considerations you impose. Therefore you can run calculations on a polymer based on the calculations of the corresponding monomer (1D replication). The same holds true for a surface (2D replication) or a crystalline solid (3D). The problem is getting the band structure of the solid which could be obtained as a result of a (very demanding) DFT calculation in which the MOs would get so packed they would constitute a band.
      I would suggest to get another software such as CRYSTAL but PBC in G09 could be a great first step in calculating the electronic structure of a solid.

      Hope this helps

      Thanks for reading!

      Reply
      • jyotsna arora | February 11, 2012 at 7:43 AM

        Dear Alam,

        i am trying to do DFT calculation of TiO2 crystal for interaction qith simple molecules like water
        But in doing so using G09 (w) when I’m taking / cleaving the crystal from a particular surface like 0 0 1 surface and interacting the water molecule

        the error is

        “Symmetry turned off by external request
        Symmetry turned off
        Cannot cope with the ghost atoms or with translational vectors”

        Do I have to give a PBC calculation for the crystal
        Also how do I see the interacting atoms as it is a symmetrical structure and on cleaving the infinte structure still remains

        Do I have to saturate the O ends of TiO2 with hydrogen/ make it a double bond?

        Regards
        Jyotsna

  17. Jomon | October 25, 2011 at 3:34 AM

    Hello sir,
    Please let me know ho to calculate EPR parameters (hyperfine splitting constants, g-tensor) using gaussian 03..

    thanking
    you
    Jo

    Reply
  18. B enghodbane soraya | October 26, 2011 at 9:33 AM

    Hello sir,
    i hope to know how can an intramolecular H-bond in guest molecule effect i the inclusion complex

    Reply
    • joaquinbarroso | December 20, 2011 at 10:35 PM

      Try calculating the wiberg bond index between those atoms involved. Find the procedure in the post with the NBO calculations in this blog.

      I hope this helps

      Reply
  19. Benghodbane soraya | October 26, 2011 at 9:43 AM

    Hello sir,
    I hope to know the relationships with the inclusion and the intramolecular h bond in guest molecule

    Reply
  20. Benghodbane soraya | October 26, 2011 at 9:44 AM

    please can you explain to me the relationships with the inclusion and the intramoleclar H-bond

    Reply
  21. Mohammad | November 3, 2011 at 6:59 AM

    I want to calculate a TS between SSOO, can you help me how to design this and how I can obtain this?

    Thanks

    Reply
  22. srinivasulu | November 24, 2011 at 11:08 AM

    Hello sir

    this srinu i am very new to this gaussian(learning now) i have been trying to optimize the transition state of aldehydic hydrogen abstraction with chlorine atom. but its forming always product i am using mpwb1k level of theory 6-31+g(d,p) basis set.please help me_

    Reply
  23. Ermi | November 27, 2011 at 8:49 PM

    Dear Dr. Joaquin;
    recently I was trying to study the Electrochemical reduction mechanism for one solvent in lithium ion battery, when I try to scan one of the bonds of the molecule I came up with a strange PES. It seems the molecule undergo a very enormous change in structure from one particular point to the next. when I try to find the TS for this bond cleavage, i always end up with convergence error and multiple imaginary frequency.I have used all of the available methods in G09 [TS(berry,QST2,QST3)], to search for the transition state but end up with failure.could you suggest any idea? for your information I have attached bellow the output for the scan of the bond i have mentioned above. Hope to hear from you soon.I thank you for your help.

    —————————-

    Entering Gaussian System, Link 0=/pkg/chem/gaussian/g09/g09
    Initial command:
    /pkg/chem/gaussian/g09c01/g09/l1.exe /work/j14erm00/ScanREDSMD_PS_LI_Test.gjf.36239/Gau-45831.inp -scrdir=/work/j14erm00/ScanREDSMD_PS_LI_Test.gjf.36239/
    Entering Link 1 = /pkg/chem/gaussian/g09c01/g09/l1.exe PID= 45834.

    Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2011,
    Gaussian, Inc. All Rights Reserved.

    This is part of the Gaussian(R) 09 program. It is based on
    the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.),
    the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.),
    the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.),
    the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.),
    the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.),
    the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.),
    the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon
    University), and the Gaussian 82(TM) system (copyright 1983,
    Carnegie Mellon University). Gaussian is a federally registered
    trademark of Gaussian, Inc.

    This software contains proprietary and confidential information,
    including trade secrets, belonging to Gaussian, Inc.

    This software is provided under written license and may be
    used, copied, transmitted, or stored only in accord with that
    written license.

    The following legend is applicable only to US Government
    contracts under FAR:

    RESTRICTED RIGHTS LEGEND

    Use, reproduction and disclosure by the US Government is
    subject to restrictions as set forth in subparagraphs (a)
    and (c) of the Commercial Computer Software – Restricted
    Rights clause in FAR 52.227-19.

    Gaussian, Inc.
    340 Quinnipiac St., Bldg. 40, Wallingford CT 06492

    —————————————————————
    Warning — This program may not be used in any manner that
    competes with the business of Gaussian, Inc. or will provide
    assistance to any competitor of Gaussian, Inc. The licensee
    of this program is prohibited from giving any competitor of
    Gaussian, Inc. access to this program. By using this program,
    the user acknowledges that Gaussian, Inc. is engaged in the
    business of creating and licensing software in the field of
    computational chemistry and represents and warrants to the
    licensee that it is not a competitor of Gaussian, Inc. and that
    it will not use this program in any manner prohibited above.
    —————————————————————

    Cite this work as:
    Gaussian 09, Revision C.01,
    M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria,
    M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci,
    G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian,
    A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada,
    M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima,
    Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr.,
    J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers,
    K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand,
    K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi,
    M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross,
    V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann,
    O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski,
    R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth,
    P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels,
    O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski,
    and D. J. Fox, Gaussian, Inc., Wallingford CT, 2010.

    ******************************************
    Gaussian 09: AM64L-G09RevC.01 23-Sep-2011
    24-Nov-2011
    ******************************************
    %nprocshared=48
    Will use up to 48 processors via shared memory.
    %mem=100MW
    %chk=ScanREDSMD_PS_LI_Test.chk
    ———————————————————————-
    # opt=modredundant ub3lyp/6-311++g(d,p) scrf=(read,smd) nosymm geom=co
    nnectivity
    ———————————————————————-
    1/14=-1,18=120,19=15,26=3,38=1,40=2,57=2/1,3;
    2/9=110,12=2,15=1,17=6,18=5,40=1/2;
    3/5=4,6=6,7=1111,11=2,16=1,25=1,30=1,70=32203,71=1,72=1,74=-5,116=2/1,2,3;
    4//1;
    5/5=2,38=5/2;
    6/7=2,8=2,9=2,10=2,28=1/1;
    7/30=1/1,2,3,16;
    1/14=-1,18=20,19=15/3(2);
    2/9=110,15=1/2;
    99//99;
    2/9=110,15=1/2;
    3/5=4,6=6,7=1111,11=2,16=1,25=1,30=1,70=32205,71=1,74=-5,116=2/1,2,3;
    4/5=5,16=3/1;
    5/5=2,38=5/2;
    7/30=1/1,2,3,16;
    1/14=-1,18=20,19=15/3(-5);
    2/9=110,15=1/2;
    6/7=2,8=2,9=2,10=2,19=2,28=1/1;
    99/9=1/99;
    ——————-
    Title Card Required
    ——————-
    Charge = 0 Multiplicity = 2
    Symbolic Z-Matrix:
    C -1.86137 -0.77246 0.16807
    C -1.85822 0.75291 0.1256
    C -0.52942 1.14829 -0.51463
    H -2.52829 -1.18787 0.91961
    H -2.05294 -1.22021 -0.80803
    H -1.93454 1.16222 1.13434
    H -2.69356 1.1241 -0.46935
    H -0.51836 1.02509 -1.59842
    H -0.14793 2.12833 -0.23121
    O 1.46419 -0.68985 -0.91046
    O 1.32772 0.34056 1.34796
    O -0.50209 -1.18338 0.58538
    S 0.62244 -0.09492 0.14661
    Li 1.76854 -1.79898 -2.37947

    The following ModRedundant input section has been read:
    B 3 13 S 25 0.0500

    GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
    Berny optimization.
    Initialization pass.
    —————————-
    ! Initial Parameters !
    ! (Angstroms and Degrees) !
    ————————– ————————–
    ! Name Definition Value Derivative Info. !
    ——————————————————————————–
    ! R1 R(1,2) 1.526 estimate D2E/DX2 !
    ! R2 R(1,4) 1.0873 estimate D2E/DX2 !
    ! R3 R(1,5) 1.0908 estimate D2E/DX2 !
    ! R4 R(1,12) 1.4801 estimate D2E/DX2 !
    ! R5 R(2,3) 1.5271 estimate D2E/DX2 !
    ! R6 R(2,6) 1.0913 estimate D2E/DX2 !
    ! R7 R(2,7) 1.0907 estimate D2E/DX2 !
    ! R8 R(3,8) 1.0908 estimate D2E/DX2 !
    ! R9 R(3,9) 1.0892 estimate D2E/DX2 !
    ! R10 R(3,13) 1.8192 Scan !
    ! R11 R(10,13) 1.4764 estimate D2E/DX2 !
    ! R12 R(10,14) 1.8657 estimate D2E/DX2 !
    ! R13 R(11,13) 1.4596 estimate D2E/DX2 !
    ! R14 R(12,13) 1.6254 estimate D2E/DX2 !
    ! A1 A(2,1,4) 113.7296 estimate D2E/DX2 !
    ! A2 A(2,1,5) 112.6912 estimate D2E/DX2 !
    ! A3 A(2,1,12) 106.4677 estimate D2E/DX2 !
    ! A4 A(4,1,5) 110.7299 estimate D2E/DX2 !
    ! A5 A(4,1,12) 105.2099 estimate D2E/DX2 !
    ! A6 A(5,1,12) 107.4345 estimate D2E/DX2 !
    ! A7 A(1,2,3) 105.7996 estimate D2E/DX2 !
    ! A8 A(1,2,6) 110.4298 estimate D2E/DX2 !
    ! A9 A(1,2,7) 110.72 estimate D2E/DX2 !
    ! A10 A(3,2,6) 110.5659 estimate D2E/DX2 !
    ! A11 A(3,2,7) 110.465 estimate D2E/DX2 !
    ! A12 A(6,2,7) 108.8459 estimate D2E/DX2 !
    ! A13 A(2,3,8) 113.337 estimate D2E/DX2 !
    ! A14 A(2,3,9) 115.3819 estimate D2E/DX2 !
    ! A15 A(2,3,13) 102.8049 estimate D2E/DX2 !
    ! A16 A(8,3,9) 110.8911 estimate D2E/DX2 !
    ! A17 A(8,3,13) 106.1131 estimate D2E/DX2 !
    ! A18 A(9,3,13) 107.37 estimate D2E/DX2 !
    ! A19 A(13,10,14) 153.674 estimate D2E/DX2 !
    ! A20 A(1,12,13) 111.9227 estimate D2E/DX2 !
    ! A21 A(3,13,10) 112.0927 estimate D2E/DX2 !
    ! A22 A(3,13,11) 113.6555 estimate D2E/DX2 !
    ! A23 A(3,13,12) 96.7591 estimate D2E/DX2 !
    ! A24 A(10,13,11) 115.7237 estimate D2E/DX2 !
    ! A25 A(10,13,12) 108.5343 estimate D2E/DX2 !
    ! A26 A(11,13,12) 108.1758 estimate D2E/DX2 !
    ! D1 D(4,1,2,3) 157.3445 estimate D2E/DX2 !
    ! D2 D(4,1,2,6) 37.6758 estimate D2E/DX2 !
    ! D3 D(4,1,2,7) -82.951 estimate D2E/DX2 !
    ! D4 D(5,1,2,3) -75.578 estimate D2E/DX2 !
    ! D5 D(5,1,2,6) 164.7534 estimate D2E/DX2 !
    ! D6 D(5,1,2,7) 44.1266 estimate D2E/DX2 !
    ! D7 D(12,1,2,3) 41.954 estimate D2E/DX2 !
    ! D8 D(12,1,2,6) -77.7147 estimate D2E/DX2 !
    ! D9 D(12,1,2,7) 161.6585 estimate D2E/DX2 !
    ! D10 D(2,1,12,13) -28.1798 estimate D2E/DX2 !
    ! D11 D(4,1,12,13) -149.1929 estimate D2E/DX2 !
    ! D12 D(5,1,12,13) 92.782 estimate D2E/DX2 !
    ! D13 D(1,2,3,8) 77.3767 estimate D2E/DX2 !
    ! D14 D(1,2,3,9) -153.2365 estimate D2E/DX2 !
    ! D15 D(1,2,3,13) -36.7044 estimate D2E/DX2 !
    ! D16 D(6,2,3,8) -163.0441 estimate D2E/DX2 !
    ! D17 D(6,2,3,9) -33.6574 estimate D2E/DX2 !
    ! D18 D(6,2,3,13) 82.8748 estimate D2E/DX2 !
    ! D19 D(7,2,3,8) -42.4952 estimate D2E/DX2 !
    ! D20 D(7,2,3,9) 86.8916 estimate D2E/DX2 !
    ! D21 D(7,2,3,13) -156.5763 estimate D2E/DX2 !
    ! D22 D(2,3,13,10) 132.3424 estimate D2E/DX2 !
    ! D23 D(2,3,13,11) -94.0907 estimate D2E/DX2 !
    ! D24 D(2,3,13,12) 19.1657 estimate D2E/DX2 !
    ! D25 D(8,3,13,10) 13.0996 estimate D2E/DX2 !
    ! D26 D(8,3,13,11) 146.6665 estimate D2E/DX2 !
    ! D27 D(8,3,13,12) -100.0771 estimate D2E/DX2 !
    ! D28 D(9,3,13,10) -105.5384 estimate D2E/DX2 !
    ! D29 D(9,3,13,11) 28.0284 estimate D2E/DX2 !
    ! D30 D(9,3,13,12) 141.2848 estimate D2E/DX2 !
    ! D31 D(14,10,13,3) -73.9297 estimate D2E/DX2 !
    ! D32 D(14,10,13,11) 153.5211 estimate D2E/DX2 !
    ! D33 D(14,10,13,12) 31.7378 estimate D2E/DX2 !
    ! D34 D(1,12,13,3) 5.0731 estimate D2E/DX2 !
    ! D35 D(1,12,13,10) -110.9792 estimate D2E/DX2 !
    ! D36 D(1,12,13,11) 122.7299 estimate D2E/DX2 !
    ——————————————————————————–
    Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-06
    Number of optimizations in scan= 26
    Number of steps in this run= 86 maximum allowed number of steps= 100.
    GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

    Input orientation:
    ———————————————————————
    Center Atomic Atomic Coordinates (Angstroms)
    Number Number Type X Y Z
    ———————————————————————
    1 6 0 -1.861372 -0.772462 0.168066
    2 6 0 -1.858224 0.752908 0.125603
    3 6 0 -0.529424 1.148285 -0.514631
    4 1 0 -2.528287 -1.187874 0.919605
    5 1 0 -2.052937 -1.220210 -0.808025
    6 1 0 -1.934542 1.162221 1.134343
    7 1 0 -2.693560 1.124098 -0.469354
    8 1 0 -0.518361 1.025093 -1.598423
    9 1 0 -0.147931 2.128331 -0.231214
    10 8 0 1.464185 -0.689845 -0.910456
    11 8 0 1.327719 0.340562 1.347956
    12 8 0 -0.502090 -1.183380 0.585381
    13 16 0 0.622437 -0.094916 0.146614
    14 3 0 1.768536 -1.798981 -2.379467
    ———————————————————————
    Distance matrix (angstroms):
    1 2 3 4 5
    1 C 0.000000
    2 C 1.525964 0.000000
    3 C 2.435042 1.527066 0.000000
    4 H 1.087269 2.201376 3.392658 0.000000
    5 H 1.090839 2.191522 2.831420 1.792124 0.000000
    6 H 2.163803 1.091292 2.166487 2.433432 3.076165
    7 H 2.166975 1.090661 2.164745 2.702173 2.453747
    8 H 2.855760 2.200360 1.090827 3.908643 2.832144
    9 H 3.392625 2.223558 1.089198 4.241190 3.895444
    10 O 3.497051 3.767407 2.740415 4.420067 3.558360
    11 O 3.577885 3.437209 2.751477 4.169938 4.302685
    12 O 1.480085 2.408258 2.578262 2.053582 2.085201
    13 S 2.574653 2.621627 1.819224 3.423322 3.055364
    14 Li 4.551911 5.093221 4.176675 5.451607 4.172297
    6 7 8 9 10
    6 H 0.000000
    7 H 1.774657 0.000000
    8 H 3.080971 2.452772 0.000000
    9 H 2.447467 2.746893 1.795442 0.000000
    10 O 4.377522 4.557609 2.710129 3.316987 0.000000
    11 O 3.370920 4.481878 3.543691 2.804896 2.486119
    12 O 2.802699 3.352531 3.105900 3.429240 2.519393
    13 S 3.015650 3.586258 2.366642 2.383075 1.476441
    14 Li 5.901556 5.665971 3.716897 4.869457 1.865692
    11 12 13 14
    11 O 0.000000
    12 O 2.500424 0.000000
    13 S 1.459550 1.625371 0.000000
    14 Li 4.320376 3.784842 3.255528 0.000000
    Symmetry turned off by external request.
    Stoichiometry C3H6LiO3S(2)
    Framework group C1[X(C3H6LiO3S)]
    Deg. of freedom 36
    Full point group C1 NOp 1
    Rotational constants (GHZ): 2.9214404 1.7299299 1.5284072
    Standard basis: 6-311++G(d,p) (5D, 7F)
    Integral buffers will be 131072 words long.
    Raffenetti 2 integral format.
    Two-electron integral symmetry is turned off.
    226 basis functions, 356 primitive gaussians, 234 cartesian basis functions
    34 alpha electrons 33 beta electrons
    nuclear repulsion energy 465.1305969305 Hartrees.
    NAtoms= 14 NActive= 14 NUniq= 14 SFac= 1.00D+00 NAtFMM= 60 NAOKFM=F Big=F
    Using the following non-standard input for PCM:
    eps=64.9
    — end of non-standard input.
    ——————————————————————————
    Polarizable Continuum Model (PCM)
    =================================
    Model : PCM.
    Atomic radii : SMD-Coulomb.
    Polarization charges : Total charges.
    Charge compensation : None.
    Solution method : Matrix inversion.
    Cavity type : VdW (van der Waals Surface) (Alpha=1.000).
    Cavity algorithm : GePol (No added spheres)
    Default sphere list used, NSphG= 14.
    Lebedev-Laikov grids with approx. 5.0 points / Ang**2.
    Smoothing algorithm: Karplus/York (Gamma=1.0000).
    Polarization charges: spherical gaussians, with
    point-specific exponents (IZeta= 3).
    Self-potential: point-specific (ISelfS= 7).
    Self-field : sphere-specific E.n sum rule (ISelfD= 2).
    1st derivatives : Analytical E(r).r(x)/FMM algorithm (CHGder, D1EAlg=3).
    Cavity 1st derivative terms included.
    Solvent : Water, Eps= 64.900000 Eps(inf)= 1.777849
    ——————————————————————————
    Spheres list:
    ISph on Nord Re0 Alpha Xe Ye Ze
    1 C 1 1.850 1.000 -1.861372 -0.772462 0.168066
    2 C 2 1.850 1.000 -1.858224 0.752908 0.125603
    3 C 3 1.850 1.000 -0.529424 1.148285 -0.514631
    4 H 4 1.200 1.000 -2.528287 -1.187874 0.919605
    5 H 5 1.200 1.000 -2.052937 -1.220210 -0.808025
    6 H 6 1.200 1.000 -1.934542 1.162221 1.134343
    7 H 7 1.200 1.000 -2.693560 1.124098 -0.469354
    8 H 8 1.200 1.000 -0.518361 1.025093 -1.598423
    9 H 9 1.200 1.000 -0.147931 2.128331 -0.231214
    10 O 10 1.520 1.000 1.464185 -0.689845 -0.910456
    11 O 11 1.520 1.000 1.327719 0.340562 1.347956
    12 O 12 1.520 1.000 -0.502090 -1.183380 0.585381
    13 S 13 2.490 1.000 0.622437 -0.094916 0.146614
    14 Li 14 1.820 1.000 1.768536 -1.798981 -2.379467
    ——————————————————————————
    ——————————————————————————
    Atomic radii for non-electrostatic terms: SMD-CDS.
    ——————————————————————————
    Nuclear repulsion after PCM non-electrostatic terms = 465.1376191418 Hartrees.
    One-electron integrals computed using PRISM.
    PrsmSu: requested number of processors reduced to: 33 ShMem 1 Linda.
    NBasis= 226 RedAO= T NBF= 226
    NBsUse= 226 1.00D-06 NBFU= 226
    Harris functional with IExCor= 402 diagonalized for initial guess.
    ExpMin= 7.40D-03 ExpMax= 9.34D+04 ExpMxC= 3.17D+03 IAcc=3 IRadAn= 5 AccDes= 0.00D+00
    HarFok: IExCor= 402 AccDes= 0.00D+00 IRadAn= 5 IDoV= 1
    ScaDFX= 1.000000 1.000000 1.000000 1.000000
    FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0
    NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T
    Omega= 0.000000 0.000000 1.000000 0.000000 0.000000 ICntrl= 500 IOpCl= 0
    NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
    I1Cent= 4 NGrid= 0.
    Symmetry not used in FoFCou.
    Initial guess = 0.0000 = 0.0000 = 0.5000 = 0.7500 S= 0.5000
    Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
    Requested convergence on MAX density matrix=1.00D-06.
    Requested convergence on energy=1.00D-06.
    No special actions if energy rises.
    Restarting incremental Fock formation.
    Error on total polarization charges = 0.14895
    SCF Done: E(UB3LYP) = -749.374645876 A.U. after 22 cycles
    Convg = 0.1108D-08 -V/T = 2.0025
    = 0.0000 = 0.0000 = 0.5000 = 0.7500 S= 0.5000
    = 0.000000000000E+00
    SMD-CDS (non-electrostatic) energy (kcal/mol) = 4.41
    (included in total energy above)
    Annihilation of the first spin contaminant:
    S**2 before annihilation 0.7500, after 0.7500

    **********************************************************************

    Population analysis using the SCF density.

    **********************************************************************

    Alpha occ. eigenvalues — -89.10691 -19.19272 -19.16137 -19.15493 -10.24660
    Alpha occ. eigenvalues — -10.22952 -10.19747 -8.16861 -6.13233 -6.13083
    Alpha occ. eigenvalues — -6.12852 -1.96876 -1.17700 -1.07007 -1.04768
    Alpha occ. eigenvalues — -0.83390 -0.76825 -0.65053 -0.62968 -0.54949
    Alpha occ. eigenvalues — -0.54467 -0.51851 -0.48646 -0.46546 -0.46339
    Alpha occ. eigenvalues — -0.41244 -0.40708 -0.39359 -0.37754 -0.37360
    Alpha occ. eigenvalues — -0.35075 -0.34531 -0.31930 -0.09143
    Alpha virt. eigenvalues — -0.00829 -0.00378 -0.00003 0.00943 0.01451
    Alpha virt. eigenvalues — 0.01700 0.02340 0.02653 0.02970 0.03401
    Alpha virt. eigenvalues — 0.03602 0.04410 0.04657 0.05443 0.05808
    Alpha virt. eigenvalues — 0.06180 0.07138 0.08156 0.08461 0.09517
    Alpha virt. eigenvalues — 0.09848 0.10717 0.11485 0.11771 0.12034
    Alpha virt. eigenvalues — 0.12687 0.13314 0.13490 0.13984 0.14285
    Alpha virt. eigenvalues — 0.14750 0.15266 0.15615 0.16231 0.17004
    Alpha virt. eigenvalues — 0.17591 0.18434 0.19447 0.20589 0.22242
    Alpha virt. eigenvalues — 0.24278 0.25200 0.25993 0.26033 0.27512
    Alpha virt. eigenvalues — 0.27813 0.29513 0.29960 0.30317 0.31327
    Alpha virt. eigenvalues — 0.31980 0.32844 0.33693 0.35112 0.35498
    Alpha virt. eigenvalues — 0.36480 0.37241 0.38149 0.38518 0.40963
    Alpha virt. eigenvalues — 0.42177 0.45943 0.46990 0.47408 0.48266
    Alpha virt. eigenvalues — 0.49130 0.51203 0.53560 0.54483 0.55958
    Alpha virt. eigenvalues — 0.57626 0.59336 0.59766 0.61572 0.63343
    Alpha virt. eigenvalues — 0.65140 0.66662 0.67273 0.67769 0.69766
    Alpha virt. eigenvalues — 0.71072 0.72030 0.74480 0.75023 0.78715
    Alpha virt. eigenvalues — 0.82894 0.85216 0.86264 0.94930 0.97633
    Alpha virt. eigenvalues — 0.99814 1.02044 1.02652 1.07361 1.08238
    Alpha virt. eigenvalues — 1.10039 1.10766 1.15368 1.17195 1.17724
    Alpha virt. eigenvalues — 1.20331 1.21734 1.24762 1.25658 1.30727
    Alpha virt. eigenvalues — 1.38160 1.43634 1.47998 1.53442 1.54737
    Alpha virt. eigenvalues — 1.55662 1.58105 1.60877 1.61509 1.64152
    Alpha virt. eigenvalues — 1.64343 1.66044 1.68658 1.70321 1.73714
    Alpha virt. eigenvalues — 1.76909 1.77724 1.81679 1.82726 1.87015
    Alpha virt. eigenvalues — 1.90984 1.94895 1.96918 2.03946 2.10522
    Alpha virt. eigenvalues — 2.13401 2.17765 2.24157 2.28652 2.30099
    Alpha virt. eigenvalues — 2.45435 2.47403 2.52286 2.53762 2.61038
    Alpha virt. eigenvalues — 2.63909 2.68755 2.72003 2.72722 2.76566
    Alpha virt. eigenvalues — 2.77319 2.79351 2.80424 2.80734 2.81416
    Alpha virt. eigenvalues — 2.82868 2.85551 2.88774 2.90354 2.93089
    Alpha virt. eigenvalues — 2.99644 3.01749 3.06362 3.08768 3.14689
    Alpha virt. eigenvalues — 3.20422 3.27781 3.32146 3.50262 3.55763
    Alpha virt. eigenvalues — 3.68144 3.76763 3.78750 3.89991 3.93994
    Alpha virt. eigenvalues — 4.14599 4.19865 4.95324 4.99528 5.01679
    Alpha virt. eigenvalues — 5.02840 5.05381 5.08733 5.18741 5.32898
    Alpha virt. eigenvalues — 5.39351 8.15128 17.25302 17.38804 17.42616
    Alpha virt. eigenvalues — 23.80474 23.85862 23.89085 49.83580 49.84859
    Alpha virt. eigenvalues — 49.89346 189.27097
    Beta occ. eigenvalues — -89.10689 -19.19265 -19.16103 -19.15486 -10.24656
    Beta occ. eigenvalues — -10.22944 -10.19747 -8.16858 -6.13231 -6.13080
    Beta occ. eigenvalues — -6.12849 -1.96269 -1.17678 -1.06988 -1.04735
    Beta occ. eigenvalues — -0.83380 -0.76810 -0.65044 -0.62946 -0.54922
    Beta occ. eigenvalues — -0.54456 -0.51834 -0.48636 -0.46532 -0.46328
    Beta occ. eigenvalues — -0.41229 -0.40699 -0.39345 -0.37739 -0.37352
    Beta occ. eigenvalues — -0.35047 -0.34521 -0.31912
    Beta virt. eigenvalues — -0.02223 0.00001 0.00095 0.00835 0.01508
    Beta virt. eigenvalues — 0.01638 0.02562 0.02714 0.03223 0.03487
    Beta virt. eigenvalues — 0.03914 0.04009 0.04499 0.04830 0.05746
    Beta virt. eigenvalues — 0.05958 0.06371 0.07619 0.08330 0.08694
    Beta virt. eigenvalues — 0.09711 0.10949 0.11047 0.11847 0.12730
    Beta virt. eigenvalues — 0.12880 0.13146 0.13690 0.13790 0.14300
    Beta virt. eigenvalues — 0.14466 0.14772 0.15555 0.15879 0.16349
    Beta virt. eigenvalues — 0.16941 0.17590 0.18552 0.20442 0.20675
    Beta virt. eigenvalues — 0.22233 0.24327 0.25284 0.25981 0.26347
    Beta virt. eigenvalues — 0.27661 0.28000 0.29509 0.29975 0.30660
    Beta virt. eigenvalues — 0.31405 0.32085 0.32907 0.33704 0.35181
    Beta virt. eigenvalues — 0.35753 0.37038 0.37613 0.38170 0.38789
    Beta virt. eigenvalues — 0.41222 0.42462 0.46127 0.47090 0.47928
    Beta virt. eigenvalues — 0.48576 0.49259 0.51541 0.54713 0.55399
    Beta virt. eigenvalues — 0.56772 0.58186 0.59644 0.60812 0.61932
    Beta virt. eigenvalues — 0.64141 0.65784 0.67430 0.67593 0.68033
    Beta virt. eigenvalues — 0.69827 0.71442 0.72069 0.74643 0.75523
    Beta virt. eigenvalues — 0.80602 0.82931 0.85429 0.86576 0.94968
    Beta virt. eigenvalues — 0.97706 0.99869 1.02085 1.02741 1.07368
    Beta virt. eigenvalues — 1.08246 1.10080 1.10773 1.15391 1.17187
    Beta virt. eigenvalues — 1.17755 1.20305 1.21727 1.24835 1.25651
    Beta virt. eigenvalues — 1.30762 1.38368 1.43643 1.48006 1.53444
    Beta virt. eigenvalues — 1.54752 1.55664 1.58108 1.60879 1.61508
    Beta virt. eigenvalues — 1.64158 1.64360 1.66052 1.68677 1.70337
    Beta virt. eigenvalues — 1.73718 1.76914 1.77730 1.81697 1.82724
    Beta virt. eigenvalues — 1.87020 1.90995 1.94909 1.96925 2.03956
    Beta virt. eigenvalues — 2.10523 2.13395 2.17767 2.24156 2.28652
    Beta virt. eigenvalues — 2.30099 2.45433 2.47397 2.52290 2.53758
    Beta virt. eigenvalues — 2.61040 2.63912 2.68752 2.72001 2.72730
    Beta virt. eigenvalues — 2.76579 2.77331 2.79361 2.80437 2.80764
    Beta virt. eigenvalues — 2.81444 2.82884 2.85559 2.88778 2.90386
    Beta virt. eigenvalues — 2.93100 2.99661 3.01769 3.06371 3.08799
    Beta virt. eigenvalues — 3.14693 3.20437 3.27783 3.32156 3.50333
    Beta virt. eigenvalues — 3.55807 3.68187 3.77132 3.79001 3.90003
    Beta virt. eigenvalues — 3.94004 4.14604 4.19867 4.95337 4.99536
    Beta virt. eigenvalues — 5.01695 5.02862 5.05392 5.08755 5.18752
    Beta virt. eigenvalues — 5.32937 5.39355 8.15136 17.25306 17.38808
    Beta virt. eigenvalues — 17.42619 23.80479 23.85868 23.89086 49.83594
    Beta virt. eigenvalues — 49.84882 49.89364 189.27100
    Condensed to atoms (all electrons):
    1 2 3 4 5 6
    1 C 6.169203 -0.479499 0.505717 0.319864 0.408688 -0.084061
    2 C -0.479499 6.220765 -0.361535 0.056981 -0.056958 0.391300
    3 C 0.505717 -0.361535 7.014693 -0.002270 -0.055739 -0.062583
    4 H 0.319864 0.056981 -0.002270 0.504522 -0.053139 -0.028979
    5 H 0.408688 -0.056958 -0.055739 -0.053139 0.527983 0.020246
    6 H -0.084061 0.391300 -0.062583 -0.028979 0.020246 0.534219
    7 H 0.015970 0.385077 0.044115 0.022528 -0.027029 -0.075791
    8 H -0.073547 0.039633 0.246128 -0.003639 0.015247 0.020960
    9 H 0.039257 -0.022055 0.363105 0.001604 0.002431 -0.022663
    10 O -0.053467 -0.013978 -0.139208 -0.013647 0.033563 0.012529
    11 O -0.014792 0.012402 -0.108178 0.003817 -0.007489 0.001273
    12 O 0.180391 0.078355 -0.246529 -0.018423 -0.066885 -0.038514
    13 S -0.604974 -0.053879 -0.626953 -0.038410 0.035939 0.099455
    14 Li -0.002664 0.012057 0.011638 -0.000929 0.010527 -0.001445
    7 8 9 10 11 12
    1 C 0.015970 -0.073547 0.039257 -0.053467 -0.014792 0.180391
    2 C 0.385077 0.039633 -0.022055 -0.013978 0.012402 0.078355
    3 C 0.044115 0.246128 0.363105 -0.139208 -0.108178 -0.246529
    4 H 0.022528 -0.003639 0.001604 -0.013647 0.003817 -0.018423
    5 H -0.027029 0.015247 0.002431 0.033563 -0.007489 -0.066885
    6 H -0.075791 0.020960 -0.022663 0.012529 0.001273 -0.038514
    7 H 0.538310 -0.035944 0.014874 -0.011890 -0.001265 0.025405
    8 H -0.035944 0.453101 -0.025639 0.023562 0.020513 -0.006230
    9 H 0.014874 -0.025639 0.437866 -0.003179 0.003076 0.018897
    10 O -0.011890 0.023562 -0.003179 8.412471 -0.204699 -0.056265
    11 O -0.001265 0.020513 0.003076 -0.204699 8.505739 -0.030728
    12 O 0.025405 -0.006230 0.018897 -0.056265 -0.030728 8.303193
    13 S -0.108245 0.054047 -0.088719 0.178053 0.103275 0.094504
    14 Li 0.001124 0.011667 0.003723 0.095805 0.006769 -0.004098
    13 14
    1 C -0.604974 -0.002664
    2 C -0.053879 0.012057
    3 C -0.626953 0.011638
    4 H -0.038410 -0.000929
    5 H 0.035939 0.010527
    6 H 0.099455 -0.001445
    7 H -0.108245 0.001124
    8 H 0.054047 0.011667
    9 H -0.088719 0.003723
    10 O 0.178053 0.095805
    11 O 0.103275 0.006769
    12 O 0.094504 -0.004098
    13 S 16.458375 -0.046906
    14 Li -0.046906 2.994694
    Mulliken atomic charges:
    1
    1 C -0.326086
    2 C -0.208666
    3 C -0.582401
    4 H 0.250120
    5 H 0.212615
    6 H 0.234055
    7 H 0.212762
    8 H 0.260141
    9 H 0.277420
    10 O -0.259649
    11 O -0.289712
    12 O -0.233074
    13 S 0.544439
    14 Li -0.091963
    Sum of Mulliken atomic charges = 0.00000
    Mulliken charges with hydrogens summed into heavy atoms:
    1
    1 C 0.136648
    2 C 0.238151
    3 C -0.044840
    10 O -0.259649
    11 O -0.289712
    12 O -0.233074
    13 S 0.544439
    14 Li -0.091963
    Sum of Mulliken charges with hydrogens summed into heavy atoms = 0.00000
    Atomic-Atomic Spin Densities.
    1 2 3 4 5 6
    1 C 0.016781 -0.009380 0.016085 0.002256 -0.014562 -0.002078
    2 C -0.009380 0.014490 -0.025628 -0.002095 0.010252 0.003650
    3 C 0.016085 -0.025628 0.045150 0.002393 -0.010233 -0.001867
    4 H 0.002256 -0.002095 0.002393 0.002334 -0.003667 -0.000660
    5 H -0.014562 0.010252 -0.010233 -0.003667 0.011836 0.001055
    6 H -0.002078 0.003650 -0.001867 -0.000660 0.001055 0.000794
    7 H 0.002439 -0.003263 0.001917 0.000563 -0.001525 -0.000571
    8 H -0.006411 0.008882 -0.015102 -0.000863 0.003813 0.000629
    9 H -0.000856 0.001134 -0.004631 -0.000276 0.000652 0.000232
    10 O 0.000715 0.000884 0.002676 0.000161 -0.001056 -0.000061
    11 O 0.000346 0.000090 0.000723 -0.000091 0.000121 0.000382
    12 O 0.003605 -0.003239 0.003635 0.001491 -0.004353 -0.000531
    13 S -0.009616 0.008087 -0.016436 -0.001621 0.008116 -0.000703
    14 Li -0.016628 0.008131 -0.017111 -0.002525 0.014669 0.000601
    7 8 9 10 11 12
    1 C 0.002439 -0.006411 -0.000856 0.000715 0.000346 0.003605
    2 C -0.003263 0.008882 0.001134 0.000884 0.000090 -0.003239
    3 C 0.001917 -0.015102 -0.004631 0.002676 0.000723 0.003635
    4 H 0.000563 -0.000863 -0.000276 0.000161 -0.000091 0.001491
    5 H -0.001525 0.003813 0.000652 -0.001056 0.000121 -0.004353
    6 H -0.000571 0.000629 0.000232 -0.000061 0.000382 -0.000531
    7 H 0.000687 -0.001042 -0.000209 0.000132 -0.000178 0.000429
    8 H -0.001042 0.005800 0.001342 -0.000871 0.000075 -0.001704
    9 H -0.000209 0.001342 0.001334 -0.000320 -0.000271 -0.000324
    10 O 0.000132 -0.000871 -0.000320 0.015013 0.001583 0.001026
    11 O -0.000178 0.000075 -0.000271 0.001583 0.004748 0.000234
    12 O 0.000429 -0.001704 -0.000324 0.001026 0.000234 0.010747
    13 S 0.000415 0.006536 0.002771 -0.013019 -0.006370 -0.009761
    14 Li -0.001093 0.012742 0.001494 -0.013474 -0.000143 -0.003811
    13 14
    1 C -0.009616 -0.016628
    2 C 0.008087 0.008131
    3 C -0.016436 -0.017111
    4 H -0.001621 -0.002525
    5 H 0.008116 0.014669
    6 H -0.000703 0.000601
    7 H 0.000415 -0.001093
    8 H 0.006536 0.012742
    9 H 0.002771 0.001494
    10 O -0.013019 -0.013474
    11 O -0.006370 -0.000143
    12 O -0.009761 -0.003811
    13 S 0.034309 0.037761
    14 Li 0.037761 0.942589
    Mulliken atomic spin densities:
    1
    1 C -0.017302
    2 C 0.011993
    3 C -0.018428
    4 H -0.002601
    5 H 0.015119
    6 H 0.000871
    7 H -0.001299
    8 H 0.013826
    9 H 0.002072
    10 O -0.006610
    11 O 0.001249
    12 O -0.002557
    13 S 0.040469
    14 Li 0.963199
    Sum of Mulliken atomic spin densities = 1.00000
    Electronic spatial extent (au): = 918.3110
    Charge= 0.0000 electrons
    Dipole moment (field-independent basis, Debye):
    X= -9.7868 Y= 6.5172 Z= 2.3853 Tot= 11.9977
    Quadrupole moment (field-independent basis, Debye-Ang):
    XX= -58.1876 YY= -65.6387 ZZ= -81.4327
    XY= 8.0625 XZ= 9.0482 YZ= -17.3518
    Traceless Quadrupole moment (field-independent basis, Debye-Ang):
    XX= 10.2321 YY= 2.7809 ZZ= -13.0130
    XY= 8.0625 XZ= 9.0482 YZ= -17.3518
    Octapole moment (field-independent basis, Debye-Ang**2):
    XXX= -72.9173 YYY= 105.9853 ZZZ= 132.8663 XYY= -37.4010
    XXY= 35.8337 XXZ= 41.7600 XZZ= -63.8386 YZZ= 79.6469
    YYZ= 59.9255 XYZ= -32.9535
    Hexadecapole moment (field-independent basis, Debye-Ang**3):
    XXXX= -751.4801 YYYY= -617.4153 ZZZZ= -982.7501 XXXY= 161.9676
    XXXZ= 187.5172 YYYX= 183.3305 YYYZ= -274.3539 ZZZX= 293.0004
    ZZZY= -366.5129 XXYY= -253.6404 XXZZ= -333.3493 YYZZ= -350.9581
    XXYZ= -126.3307 YYXZ= 130.6680 ZZXY= 150.0130
    N-N= 4.651376191418D+02 E-N=-4.041293857914D+03 KE= 1.121131217203D+03
    Isotropic Fermi Contact Couplings
    Atom a.u. MegaHertz Gauss 10(-4) cm-1
    1 C(13) 0.00011 0.11937 0.04259 0.03982
    2 C(13) 0.00003 0.03840 0.01370 0.01281
    3 C(13) 0.00502 5.64657 2.01484 1.88349
    4 H(1) -0.00003 -0.13198 -0.04709 -0.04402
    5 H(1) -0.00004 -0.18136 -0.06471 -0.06050
    6 H(1) 0.00006 0.28400 0.10134 0.09473
    7 H(1) 0.00000 0.01243 0.00444 0.00415
    8 H(1) -0.00003 -0.12796 -0.04566 -0.04268
    9 H(1) 0.00001 0.04793 0.01710 0.01599
    10 O(17) 0.05907 -35.80996 -12.77788 -11.94492
    11 O(17) 0.00386 -2.33942 -0.83476 -0.78035
    12 O(17) 0.00908 -5.50443 -1.96412 -1.83608
    13 S(33) 0.01577 5.41612 1.93261 1.80662
    14 Li(7) 0.15403 267.58424 95.48071 89.25650
    ——————————————————–
    Center —- Spin Dipole Couplings —-
    3XX-RR 3YY-RR 3ZZ-RR
    ——————————————————–
    1 Atom 0.000894 -0.001971 0.001077
    2 Atom 0.000341 -0.000321 -0.000020
    3 Atom -0.000539 0.000443 0.000097
    4 Atom 0.000359 -0.000658 0.000298
    5 Atom 0.000989 -0.001138 0.000149
    6 Atom -0.000038 -0.000086 0.000124
    7 Atom 0.000315 -0.000060 -0.000255
    8 Atom -0.000682 0.000597 0.000085
    9 Atom -0.000550 0.000745 -0.000195
    10 Atom -0.002754 0.001679 0.001075
    11 Atom -0.003651 -0.000945 0.004596
    12 Atom -0.001468 -0.001629 0.003097
    13 Atom 0.000411 0.000315 -0.000726
    14 Atom -0.006466 -0.000366 0.006832
    ——————————————————–
    XY XZ YZ
    ——————————————————–
    1 Atom 0.000088 0.000893 0.001367
    2 Atom -0.000672 -0.001092 0.000567
    3 Atom -0.002036 -0.001565 0.001968
    4 Atom -0.000154 -0.000922 0.000134
    5 Atom -0.000888 -0.001775 0.000843
    6 Atom -0.000392 -0.000481 0.000514
    7 Atom -0.000661 -0.000511 0.000354
    8 Atom -0.001650 -0.000812 0.001351
    9 Atom -0.000540 -0.000380 0.000969
    10 Atom 0.000298 0.000213 0.005413
    11 Atom -0.002235 -0.003114 0.006690
    12 Atom -0.001236 -0.003642 0.002244
    13 Atom -0.004906 -0.005165 0.004135
    14 Atom -0.001771 -0.002538 0.009495
    ——————————————————–

    ———————————————————————————
    Anisotropic Spin Dipole Couplings in Principal Axis System
    ———————————————————————————

    Atom a.u. MegaHertz Gauss 10(-4) cm-1 Axes

    Baa -0.0025 -0.337 -0.120 -0.112 0.0735 0.9258 -0.3709
    1 C(13) Bbb 0.0003 0.044 0.016 0.015 0.8251 -0.2653 -0.4988
    Bcc 0.0022 0.293 0.105 0.098 0.5601 0.2694 0.7834

    Baa -0.0009 -0.127 -0.045 -0.042 0.6493 0.0080 0.7605
    2 C(13) Bbb -0.0007 -0.095 -0.034 -0.032 0.3041 0.9138 -0.2693
    Bcc 0.0017 0.223 0.079 0.074 0.6971 -0.4061 -0.5909

    Baa -0.0021 -0.288 -0.103 -0.096 0.7913 0.6112 0.0157
    3 C(13) Bbb -0.0016 -0.218 -0.078 -0.073 0.3352 -0.4551 0.8249
    Bcc 0.0038 0.506 0.180 0.169 -0.5113 0.6475 0.5650

    Baa -0.0007 -0.363 -0.130 -0.121 0.1625 0.9865 0.0185
    4 H(1) Bbb -0.0006 -0.316 -0.113 -0.105 0.6799 -0.1255 0.7225
    Bcc 0.0013 0.679 0.242 0.227 0.7151 -0.1048 -0.6911

    Baa -0.0016 -0.830 -0.296 -0.277 0.0128 0.9015 -0.4326
    5 H(1) Bbb -0.0012 -0.650 -0.232 -0.217 0.6685 0.3141 0.6741
    Bcc 0.0028 1.480 0.528 0.494 0.7436 -0.2978 -0.5986

    Baa -0.0005 -0.270 -0.096 -0.090 -0.0022 0.7739 -0.6333
    6 H(1) Bbb -0.0004 -0.231 -0.082 -0.077 0.8437 0.3415 0.4143
    Bcc 0.0009 0.501 0.179 0.167 -0.5369 0.5334 0.6536

    Baa -0.0006 -0.307 -0.109 -0.102 0.6824 0.5291 0.5043
    7 H(1) Bbb -0.0005 -0.280 -0.100 -0.093 -0.0534 -0.6521 0.7563
    Bcc 0.0011 0.587 0.209 0.196 0.7290 -0.5430 -0.4168

    Baa -0.0018 -0.971 -0.346 -0.324 0.8025 0.5916 -0.0778
    8 H(1) Bbb -0.0009 -0.460 -0.164 -0.153 0.3621 -0.3792 0.8515
    Bcc 0.0027 1.431 0.510 0.477 -0.4743 0.7115 0.5185

    Baa -0.0008 -0.438 -0.156 -0.146 0.4477 -0.3539 0.8212
    9 H(1) Bbb -0.0007 -0.394 -0.141 -0.131 0.8429 0.4736 -0.2554
    Bcc 0.0016 0.831 0.297 0.277 -0.2985 0.8065 0.5103

    Baa -0.0040 0.293 0.104 0.098 0.0392 -0.6876 0.7251
    10 O(17) Bbb -0.0028 0.200 0.071 0.067 0.9985 -0.0006 -0.0545
    Bcc 0.0068 -0.493 -0.176 -0.164 0.0379 0.7261 0.6865

    Baa -0.0054 0.393 0.140 0.131 0.1631 0.8435 -0.5118
    11 O(17) Bbb -0.0047 0.340 0.121 0.113 0.9496 0.0066 0.3135
    Bcc 0.0101 -0.733 -0.262 -0.245 -0.2678 0.5371 0.7999

    Baa -0.0035 0.252 0.090 0.084 0.8742 -0.0051 0.4855
    12 O(17) Bbb -0.0025 0.180 0.064 0.060 0.1592 0.9477 -0.2767
    Bcc 0.0060 -0.432 -0.154 -0.144 -0.4587 0.3192 0.8293

    Baa -0.0054 -0.220 -0.079 -0.074 0.7122 0.1101 0.6933
    13 S(33) Bbb -0.0041 -0.170 -0.061 -0.057 0.3370 0.8128 -0.4752
    Bcc 0.0095 0.390 0.139 0.130 0.6158 -0.5721 -0.5417

    Baa -0.0069 -1.441 -0.514 -0.481 0.8467 0.4981 -0.1873
    14 Li(7) Bbb -0.0069 -1.433 -0.511 -0.478 -0.5104 0.6605 -0.5506
    Bcc 0.0139 2.874 1.025 0.959 -0.1506 0.5618 0.8135

    ———————————————————————————

    PrsmSu: requested number of processors reduced to: 33 ShMem 1 Linda.
    D1PCM: PCM CHGder 1st derivatives, ID1Alg=3 FixD1E=F DoIter=F DoCFld=F I1PDM=0.
    CoulSu: requested number of processors reduced to: 33 ShMem 1 Linda.
    CoulSu: requested number of processors reduced to: 34 ShMem 1 Linda.
    Calling FoFJK, ICntrl= 2127 FMM=F ISym2X=0 I1Cent= 0 IOpClX= 1 NMat=1 NMatS=1 NMatT=0.
    ——————————————————————-
    Center Atomic Forces (Hartrees/Bohr)
    Number Number X Y Z
    ——————————————————————-
    1 6 0.000018633 -0.000002943 0.000007468
    2 6 0.000005370 0.000016110 -0.000013317
    3 6 -0.000021689 -0.000004882 -0.000037361
    4 1 -0.000013829 0.000021508 0.000009957
    5 1 0.000003174 -0.000008747 0.000010956
    6 1 -0.000010729 0.000016564 -0.000027281
    7 1 0.000000808 -0.000009527 -0.000031884
    8 1 0.000017021 -0.000022040 -0.000011479
    9 1 0.000003007 -0.000004330 -0.000026869
    10 8 0.000020905 -0.000084953 0.000127550
    11 8 0.000021027 0.000032482 0.000041003
    12 8 0.000037886 0.000020451 -0.000006054
    13 16 -0.000072993 0.000044269 -0.000035549
    14 3 -0.000008590 -0.000013962 -0.000007140
    ——————————————————————-
    Cartesian Forces: Max 0.000127550 RMS 0.000032910

    GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
    Berny optimization.
    Internal Forces: Max 0.000049159 RMS 0.000013714
    Search for a local minimum.
    Step number 1 out of a maximum of 86 on scan point 1 out of 26
    All quantities printed in internal units (Hartrees-Bohrs-Radians)
    Mixed Optimization — En-DIIS/RFO-DIIS
    Second derivative matrix not updated — first step.
    ITU= 0
    Eigenvalues — 0.00547 0.00874 0.03020 0.03382 0.04253
    Eigenvalues — 0.04864 0.05111 0.05451 0.06017 0.06563
    Eigenvalues — 0.06963 0.07207 0.07384 0.08789 0.10385
    Eigenvalues — 0.11304 0.11734 0.11927 0.14665 0.15642
    Eigenvalues — 0.20767 0.21574 0.25000 0.28595 0.28901
    Eigenvalues — 0.33247 0.34664 0.34716 0.34717 0.34736
    Eigenvalues — 0.34905 0.35130 0.44697 0.85040 0.91799
    Eigenvalues — 1000.000001000.000001000.000001000.000001000.00000
    Eigenvalues — 1000.000001000.000001000.000001000.000001000.00000
    Eigenvalues — 1000.000001000.000001000.000001000.000001000.00000
    Eigenvalues — 1000.000001000.000001000.000001000.000001000.00000
    Eigenvalues — 1000.000001000.000001000.000001000.000001000.00000
    Eigenvalues — 1000.000001000.000001000.000001000.000001000.00000
    Eigenvalues — 1000.000001000.000001000.000001000.000001000.00000
    Eigenvalues — 1000.000001000.000001000.000001000.000001000.00000
    Eigenvalues — 1000.00000
    RFO step: Lambda=-1.23426458D-07 EMin= 5.47021454D-03
    Linear search not attempted — first point.
    Iteration 1 RMS(Cart)= 0.00031877 RMS(Int)= 0.00000008
    Iteration 2 RMS(Cart)= 0.00000007 RMS(Int)= 0.00000000
    Iteration 1 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000000
    Variable Old X -DE/DX Delta X Delta X Delta X New X
    (Linear) (Quad) (Total)
    R1 2.88365 0.00001 0.00000 0.00001 0.00001 2.88367
    R2 2.05464 0.00000 0.00000 0.00001 0.00001 2.05465
    R3 2.06139 0.00000 0.00000 0.00000 0.00000 2.06139
    R4 2.79696 -0.00001 0.00000 -0.00004 -0.00004 2.79692
    R5 2.88574 0.00000 0.00000 -0.00001 -0.00001 2.88573
    R6 2.06224 0.00000 0.00000 -0.00001 -0.00001 2.06223
    R7 2.06105 0.00000 0.00000 0.00000 0.00000 2.06105
    R8 2.06136 0.00000 0.00000 -0.00001 -0.00001 2.06136
    R9 2.05829 0.00000 0.00000 -0.00001 -0.00001 2.05828
    R10 3.43784 0.00000 0.00000 0.00000 0.00000 3.43784
    R11 2.79007 -0.00002 0.00000 -0.00002 -0.00002 2.79005
    R12 3.52565 0.00002 0.00000 0.00020 0.00020 3.52585
    R13 2.75815 0.00004 0.00000 0.00005 0.00005 2.75820
    R14 3.07151 -0.00005 0.00000 -0.00011 -0.00011 3.07140
    A1 1.98496 0.00000 0.00000 -0.00006 -0.00006 1.98490
    A2 1.96683 0.00000 0.00000 -0.00002 -0.00002 1.96682
    A3 1.85821 0.00001 0.00000 0.00005 0.00005 1.85827
    A4 1.93260 0.00000 0.00000 0.00000 0.00000 1.93260
    A5 1.83626 0.00000 0.00000 0.00005 0.00005 1.83631
    A6 1.87509 0.00000 0.00000 -0.00001 -0.00001 1.87507
    A7 1.84655 -0.00001 0.00000 0.00004 0.00004 1.84659
    A8 1.92736 0.00000 0.00000 -0.00003 -0.00003 1.92733
    A9 1.93243 0.00000 0.00000 -0.00005 -0.00005 1.93237
    A10 1.92974 0.00001 0.00000 0.00003 0.00003 1.92977
    A11 1.92798 0.00000 0.00000 0.00001 0.00001 1.92799
    A12 1.89972 0.00000 0.00000 0.00001 0.00001 1.89973
    A13 1.97810 0.00000 0.00000 0.00006 0.00006 1.97816
    A14 2.01379 0.00001 0.00000 0.00002 0.00002 2.01381
    A15 1.79428 -0.00001 0.00000 -0.00001 -0.00001 1.79427
    A16 1.93542 0.00000 0.00000 0.00000 0.00000 1.93542
    A17 1.85202 0.00000 0.00000 -0.00006 -0.00006 1.85197
    A18 1.87396 0.00000 0.00000 -0.00002 -0.00002 1.87394
    A19 2.68212 -0.00005 0.00000 -0.00019 -0.00019 2.68192
    A20 1.95342 0.00000 0.00000 -0.00002 -0.00002 1.95339
    A21 1.95639 -0.00001 0.00000 -0.00004 -0.00004 1.95635
    A22 1.98366 0.00002 0.00000 0.00017 0.00017 1.98383
    A23 1.68876 0.00002 0.00000 0.00007 0.00007 1.68884
    A24 2.01976 0.00000 0.00000 0.00005 0.00005 2.01981
    A25 1.89428 -0.00003 0.00000 -0.00032 -0.00032 1.89396
    A26 1.88802 0.00000 0.00000 0.00004 0.00004 1.88806
    D1 2.74618 0.00001 0.00000 -0.00007 -0.00007 2.74611
    D2 0.65757 0.00000 0.00000 -0.00011 -0.00011 0.65746
    D3 -1.44777 0.00000 0.00000 -0.00006 -0.00006 -1.44783
    D4 -1.31908 0.00000 0.00000 -0.00014 -0.00014 -1.31922
    D5 2.87549 0.00000 0.00000 -0.00018 -0.00018 2.87531
    D6 0.77015 0.00000 0.00000 -0.00013 -0.00013 0.77002
    D7 0.73223 0.00000 0.00000 -0.00013 -0.00013 0.73211
    D8 -1.35638 0.00000 0.00000 -0.00017 -0.00017 -1.35655
    D9 2.82147 0.00000 0.00000 -0.00013 -0.00013 2.82135
    D10 -0.49183 0.00001 0.00000 0.00004 0.00004 -0.49179
    D11 -2.60391 0.00001 0.00000 0.00006 0.00006 -2.60385
    D12 1.61935 0.00000 0.00000 0.00004 0.00004 1.61940
    D13 1.35048 0.00000 0.00000 0.00014 0.00014 1.35061
    D14 -2.67448 0.00000 0.00000 0.00021 0.00021 -2.67427
    D15 -0.64061 0.00000 0.00000 0.00019 0.00019 -0.64043
    D16 -2.84566 -0.00001 0.00000 0.00014 0.00014 -2.84552
    D17 -0.58743 0.00000 0.00000 0.00021 0.00021 -0.58722
    D18 1.44644 0.00000 0.00000 0.00019 0.00019 1.44662
    D19 -0.74168 0.00000 0.00000 0.00017 0.00017 -0.74151
    D20 1.51654 0.00001 0.00000 0.00025 0.00025 1.51680
    D21 -2.73277 0.00001 0.00000 0.00022 0.00022 -2.73255
    D22 2.30981 -0.00002 0.00000 -0.00047 -0.00047 2.30935
    D23 -1.64219 0.00000 0.00000 -0.00027 -0.00027 -1.64246
    D24 0.33450 0.00001 0.00000 -0.00013 -0.00013 0.33437
    D25 0.22863 -0.00002 0.00000 -0.00050 -0.00050 0.22813
    D26 2.55981 0.00000 0.00000 -0.00031 -0.00031 2.55951
    D27 -1.74667 0.00001 0.00000 -0.00017 -0.00017 -1.74684
    D28 -1.84199 -0.00002 0.00000 -0.00046 -0.00046 -1.84246
    D29 0.48919 0.00000 0.00000 -0.00027 -0.00027 0.48892
    D30 2.46589 0.00001 0.00000 -0.00013 -0.00013 2.46575
    D31 -1.29032 0.00003 0.00000 0.00076 0.00076 -1.28956
    D32 2.67945 0.00001 0.00000 0.00050 0.00050 2.67995
    D33 0.55393 0.00003 0.00000 0.00067 0.00067 0.55459
    D34 0.08854 -0.00001 0.00000 0.00005 0.00005 0.08859
    D35 -1.93695 0.00000 0.00000 0.00016 0.00016 -1.93680
    D36 2.14204 0.00002 0.00000 0.00028 0.00028 2.14232
    Item Value Threshold Converged?
    Maximum Force 0.000049 0.000450 YES
    RMS Force 0.000014 0.000300 YES
    Maximum Displacement 0.001914 0.001800 NO
    RMS Displacement 0.000319 0.001200 YES
    Predicted change in Energy=-6.171401D-08
    GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad

    Input orientation:
    ———————————————————————
    Center Atomic Atomic Coordinates (Angstroms)
    Number Number Type X Y Z
    ———————————————————————
    1 6 0 -1.861168 -0.772522 0.168039
    2 6 0 -1.858224 0.752852 0.125445
    3 6 0 -0.529363 1.148413 -0.514541
    4 1 0 -2.528153 -1.187905 0.919541
    5 1 0 -2.052604 -1.220364 -0.808034
    6 1 0 -1.934852 1.162207 1.134139
    7 1 0 -2.693507 1.123818 -0.469727
    8 1 0 -0.518039 1.025295 -1.598335
    9 1 0 -0.147981 2.128453 -0.230964
    10 8 0 1.463999 -0.689932 -0.910314
    11 8 0 1.327929 0.340611 1.348113
    12 8 0 -0.501903 -1.183290 0.585489
    13 16 0 0.622492 -0.094749 0.146788
    14 3 0 1.767523 -1.799057 -2.379641
    ———————————————————————
    Distance matrix (angstroms):
    1 2 3 4 5
    1 C 0.000000
    2 C 1.525972 0.000000
    3 C 2.435079 1.527063 0.000000
    4 H 1.087275 2.201348 3.392659 0.000000
    5 H 1.090838 2.191517 2.831520 1.792126 0.000000
    6 H 2.163783 1.091287 2.166502 2.433328 3.076125
    7 H 2.166943 1.090662 2.164748 2.702124 2.453650
    8 H 2.855910 2.200395 1.090823 3.908775 2.832393
    9 H 3.392620 2.223564 1.089195 4.241122 3.895532
    10 O 3.496628 3.767172 2.740373 4.419686 3.557853
    11 O 3.577986 3.437504 2.751646 4.170061 4.302745
    12 O 1.480067 2.408297 2.578305 2.053607 2.085175
    13 S 2.574567 2.621609 1.819224 3.423259 3.055295
    14 Li 4.551027 5.092518 4.176346 5.450775 4.171115
    6 7 8 9 10
    6 H 0.000000
    7 H 1.774660 0.000000
    8 H 3.080993 2.452779 0.000000
    9 H 2.447457 2.746999 1.795439 0.000000
    10 O 4.377487 4.557265 2.709954 3.317120 0.000000
    11 O 3.371431 4.482177 3.543719 2.805026 2.486167
    12 O 2.802806 3.352516 3.105994 3.429213 2.519047
    13 S 3.015760 3.586202 2.366593 2.383055 1.476429
    14 Li 5.901128 5.664959 3.716342 4.869425 1.865800
    11 12 13 14
    11 O 0.000000
    12 O 2.500432 0.000000
    13 S 1.459576 1.625313 0.000000
    14 Li 4.320599 3.784370 3.255550 0.000000
    Symmetry turned off by external request.
    Stoichiometry C3H6LiO3S(2)
    Framework group C1[X(C3H6LiO3S)]
    Deg. of freedom 36
    Full point group C1 NOp 1
    Rotational constants (GHZ): 2.9208687 1.7302430 1.5285153
    Standard basis: 6-311++G(d,p) (5D, 7F)
    Integral buffers will be 131072 words long.
    Raffenetti 2 integral format.
    Two-electron integral symmetry is turned off.
    226 basis functions, 356 primitive gaussians, 234 cartesian basis functions
    34 alpha electrons 33 beta electrons
    nuclear repulsion energy 465.1346733122 Hartrees.
    NAtoms= 14 NActive= 14 NUniq= 14 SFac= 1.00D+00 NAtFMM= 60 NAOKFM=F Big=F
    ——————————————————————————
    Polarizable Continuum Model (PCM)
    =================================
    Model : PCM.
    Atomic radii : SMD-Coulomb.
    Polarization charges : Total charges.
    Charge compensation : None.
    Solution method : Matrix inversion.
    Cavity type : VdW (van der Waals Surface) (Alpha=1.000).
    Cavity algorithm : GePol (No added spheres)
    Default sphere list used, NSphG= 14.
    Lebedev-Laikov grids with approx. 5.0 points / Ang**2.
    Smoothing algorithm: Karplus/York (Gamma=1.0000).
    Polarization charges: spherical gaussians, with
    point-specific exponents (IZeta= 3).
    Self-potential: point-specific (ISelfS= 7).
    Self-field : sphere-specific E.n sum rule (ISelfD= 2).
    1st derivatives : Analytical E(r).r(x)/FMM algorithm (CHGder, D1EAlg=3).
    Cavity 1st derivative terms included.
    Solvent : Water, Eps= 64.900000 Eps(inf)= 1.777849
    ——————————————————————————
    Spheres list:
    ISph on Nord Re0 Alpha Xe Ye Ze
    1 C 1 1.850 1.000 -1.861168 -0.772522 0.168039
    2 C 2 1.850 1.000 -1.858224 0.752852 0.125445
    3 C 3 1.850 1.000 -0.529363 1.148413 -0.514541
    4 H 4 1.200 1.000 -2.528153 -1.187905 0.919541
    5 H 5 1.200 1.000 -2.052604 -1.220364 -0.808034
    6 H 6 1.200 1.000 -1.934852 1.162207 1.134139
    7 H 7 1.200 1.000 -2.693507 1.123818 -0.469727
    8 H 8 1.200 1.000 -0.518039 1.025295 -1.598335
    9 H 9 1.200 1.000 -0.147981 2.128453 -0.230964
    10 O 10 1.520 1.000 1.463999 -0.689932 -0.910314
    11 O 11 1.520 1.000 1.327929 0.340611 1.348113
    12 O 12 1.520 1.000 -0.501903 -1.183290 0.585489
    13 S 13 2.490 1.000 0.622492 -0.094749 0.146788
    14 Li 14 1.820 1.000 1.767523 -1.799057 -2.379641
    ——————————————————————————
    ——————————————————————————
    Atomic radii for non-electrostatic terms: SMD-CDS.
    ——————————————————————————
    Nuclear repulsion after PCM non-electrostatic terms = 465.1416958131 Hartrees.
    One-electron integrals computed using PRISM.
    PrsmSu: requested number of processors reduced to: 33 ShMem 1 Linda.
    NBasis= 226 RedAO= T NBF= 226
    NBsUse= 226 1.00D-06 NBFU= 226
    Initial guess read from the read-write file.
    B after Tr= 0.000000 0.000000 0.000000
    Rot= 1.000000 0.000000 0.000000 0.000000 Ang= 0.00 deg.
    Initial guess = 0.0000 = 0.0000 = 0.5000 = 0.7500 S= 0.5000
    Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
    Requested convergence on MAX density matrix=1.00D-06.
    Requested convergence on energy=1.00D-06.
    No special actions if energy rises.
    Error on total polarization charges = 0.14895
    SCF Done: E(UB3LYP) = -749.374645970 A.U. after 12 cycles
    Convg = 0.4893D-08 -V/T = 2.0025
    = 0.0000 = 0.0000 = 0.5000 = 0.7500 S= 0.5000
    = 0.000000000000E+00
    SMD-CDS (non-electrostatic) energy (kcal/mol) = 4.41
    (included in total energy above)
    Annihilation of the first spin contaminant:
    S**2 before annihilation 0.7500, after 0.7500
    PrsmSu: requested number of processors reduced to: 33 ShMem 1 Linda.
    D1PCM: PCM CHGder 1st derivatives, ID1Alg=3 FixD1E=F DoIter=F DoCFld=F I1PDM=0.
    CoulSu: requested number of processors reduced to: 33 ShMem 1 Linda.
    CoulSu: requested number of processors reduced to: 34 ShMem 1 Linda.
    Calling FoFJK, ICntrl= 2127 FMM=F ISym2X=0 I1Cent= 0 IOpClX= 1 NMat=1 NMatS=1 NMatT=0.
    ——————————————————————-
    Center Atomic Forces (Hartrees/Bohr)
    Number Number X Y Z
    ——————————————————————-
    1 6 0.000003479 -0.000008081 0.000008516
    2 6 0.000000262 0.000011272 -0.000014920
    3 6 -0.000015701 -0.000002040 -0.000022706
    4 1 -0.000009697 0.000020082 0.000006568
    5 1 0.000003365 -0.000009739 0.000010071
    6 1 -0.000007590 0.000021490 -0.000026307
    7 1 0.000001842 -0.000006708 -0.000030730
    8 1 0.000013657 -0.000022253 -0.000012463
    9 1 -0.000000317 0.000000037 -0.000027244
    10 8 0.000058384 -0.000069706 0.000105079
    11 8 -0.000002115 0.000037029 0.000007002
    12 8 0.000001461 0.000031949 0.000020125
    13 16 -0.000038722 0.000004939 -0.000021753
    14 3 -0.000008309 -0.000008272 -0.000001238
    ——————————————————————-
    Cartesian Forces: Max 0.000105079 RMS 0.000026769

    GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
    Berny optimization.
    Using GEDIIS/GDIIS optimizer.
    Internal Forces: Max 0.000043083 RMS 0.000008389
    Search for a local minimum.
    Step number 2 out of a maximum of 86 on scan point 1 out of 26
    All quantities printed in internal units (Hartrees-Bohrs-Radians)
    Mixed Optimization — En-DIIS/RFO-DIIS
    Swaping is turned off.
    Update second derivatives using D2CorX and points 1 2
    DE= -9.45D-08 DEPred=-6.17D-08 R= 1.53D+00
    Trust test= 1.53D+00 RLast= 1.77D-03 DXMaxT set to 3.00D-01
    ITU= 0 0
    Eigenvalues — 0.00469 0.00862 0.01569 0.03059 0.03389
    Eigenvalues — 0.04874 0.05111 0.05454 0.06015 0.06663
    Eigenvalues — 0.06970

    Reply
  24. Partha | December 2, 2011 at 11:33 AM

    Dear Dr. Joaquin,
    I am trying to optimize a structure of CdCl4 with two cation at a distant apart.
    Following is my input:
    %chk=a.chk
    %nproc=4
    %mem=120MW
    #p b3lyp/Gen pseudo=read opt scf(tight,maxcycle=1000)

    Calculation

    0 1
    Cd -0.00000000 0.00000000 -0.00000000
    Cl 1.86600000 1.89125000 0.29318000
    Cl -0.00000000 -0.37522000 2.49421000
    …………………..
    ………………..
    C N H 0
    6-31G(d)
    ****
    Cl 0
    6-31G++(d)
    ****
    Cd 0
    LANL2DZ
    ****

    Cd 0
    LANL2DZ

    But I am getting a structure which is away from the crystal structure.
    If I include counterpoise keyword and specify the fragment I am getting an error message
    Cd atom has 48 electrons but 18 basis set is defined. This is less than minimal basis set.
    Yet it is calculating the structure but the the mulliken charge I am specifying is not conserved.
    Kindly help.

    Reply
    • joaquinbarroso | December 20, 2011 at 10:00 PM

      Ok, you have two different problems here:

      1) Optimizing the structure means you will find the structure with the lowest (within reason) energy possible; crystal structures are often not since they are restrained by the crystal field. Taking them out of the crystal allows them to be relaxed which explains why both structures are different.
      2) the counterpoise keyword calculates how the electrons from one fragment populate the basis set functions of the other fragment. The method doesn’t work with pseudopotentials like LANL2DZ (which replaces the core of 30 electrons so the calculation is performed faster) but the method knows that Cd has 48 electrons and only finds space for 18 so it crashes.

      I hope this helps

      Reply
  25. Dai | December 4, 2011 at 7:41 AM

    Hi Dr.!
    I’m a newcomer on Comput. Chem. I wonder if you could help me with this problem. Have you use Molden 3.4 program yet? I use this program to visualize the MO of tetraaluminium dianion but I could not obtain the HOMO, HOMO-1 or any MO pictures look like on this paper DOI: 10.1126/science.291.5505.859 despite the fact that I used the same program (G03W) and Method in my calculation. Could you help me?
    Many Thanks for any Reply!

    Reply
    • joaquinbarroso | December 20, 2011 at 9:50 PM

      I’m not an expert on Molden but my guess is that the program can’t find the basis set and therefore can’t generate the MOs from the calculated coefficients. Try using the following options in your calculation: gfprint gfoldprint and gfinput. all of them print the basis set in different formats, molden will be able to read one of them and then generate the MOs

      I hope this helps!

      Reply
  26. Hosop | December 5, 2011 at 8:01 PM

    Hi Dr.
    I’m using Gaussian with NBO analysis. I’m running optimization with NBO. But usually I got the following error message: ” NBStor is confused about NOcc. ”
    I saw some questions about this on your website, so I tried to change the basis set, but it occurs some times.
    Is there any difference if I do the optimization first, then do the NBO analysis? I did the optimization with NBO, which means before opt, NBO is performed, and after geometry optimization, NBO is performed. I’m using one molecule with charge 0, -1, +1. Although it works with charge 0 based on some basis set, it doesn’t work with charge -1 based on the same basis.
    Is it ok to optimize for geometry, then use the optimized geometry with NBO in energy calculation?

    Reply
    • joaquinbarroso | December 20, 2011 at 10:20 PM

      It is correct to do it that way but you won’t find any difference in the result. You have a basis set issue which can’t be overcome and that is due to the charge. Try it your way and if it works PLEASE let me know, ok?

      Have a nice day!

      Reply
  27. Saied | December 28, 2011 at 1:43 PM

    Hello sir
    i trying to calculate Fukui function for some pyridine derivatives but i have a problem. assuming i want to calculate the Fukui function of pyridine so three calculation must be performed
    first, for pyridine which is the neutral molecule to be analyzed of N electron system
    second is the negative ion of pyridine (N+1) system——-???????
    third is the positive ion of pyridine (N-1) system——–??????
    does the input file of the second and third calculation is the same of the first but just only change the charge of the system fro 0 to -1 and +1
    or what?

    Reply
  28. Saied | December 28, 2011 at 1:58 PM

    hello sir
    sorry for the incomplete message, i just want to ask about what is he N system, N-1 and N+1 systems used for pyridine?
    i tried to do the calculations using g03 at DFT/B3LYP level for pyridine its ok
    but i dont know what are the N-1 and N+1 species should be calculated.

    best regard
    Dr Saied Soliman

    Reply
  29. Enrico D'Ortenzio | December 31, 2011 at 9:09 AM

    Hello,
    i’m trying to optimize the structure of Ir(ppy)3 and then i want to calculte uv vis spectr awith varying th density functionals…
    i try to use GEN keyword to set basis sets for Iridium and the pop=(readradii) for it.
    but when i run the job i get errors
    this is the input file:

    %chk=C:\Users\Enrico D\Desktop\Ir(ppy)3 testgrd.chk
    # opt freq td rb3lyp/gen geom=connectivity int=ultrafine
    pop=(readradii,mk) pseudo=read

    Title Card Required

    0 1
    C -3.99749000 -2.98380300 0.00000000
    C -4.15709000 -1.63958500 0.00000000
    C -2.90822600 -0.74768400 0.00000000
    C -1.67055100 -1.23449400 0.00000000
    C -1.48668300 -2.76506200 0.00000000
    C -2.57441300 -3.58229800 0.00000000
    C -2.91748200 0.72025200 0.00000000
    C -4.02164900 1.49664600 0.00000000
    C -3.83063900 3.01655200 0.00000000
    C -2.56850500 3.50396400 0.00000000
    C -1.37319400 2.52360000 0.00000000
    N -1.57201600 1.23716300 0.00000000
    C -1.49898000 -2.45091700 0.00000000
    C -1.65118700 2.67012600 0.00000000
    N -0.28544700 -1.97986700 0.00000000
    C 0.83493000 -2.88661100 0.00000000
    C 0.71469000 -4.23096000 0.00000000
    C -0.69702200 -4.82555100 0.00000000
    C -1.75026000 -3.97629300 0.00000000
    C -1.81514700 4.02072500 0.00000000
    C -0.58536300 4.95399800 0.00000000
    C 0.65862700 4.42015600 0.00000000
    C 0.80666600 2.89257300 0.00000000
    C -0.23376500 2.06410800 0.00000000
    C 2.10159300 -2.14477600 0.00000000
    C 2.08253600 2.16647700 0.00000000
    C 3.30703300 2.73434500 0.00000000
    C 4.52771400 1.80883200 0.00000000
    C 4.31866200 0.47210600 0.00000000
    C 2.87194500 -0.07273300 0.00000000
    N 1.85736100 0.74280900 0.00000000
    C 3.13809300 0.09483200 0.00000000
    C 1.90442100 -0.82952500 0.00000000
    C 4.38967500 -0.43867700 0.00000000
    C 4.58279900 -1.97036800 0.00000000
    C 3.49838600 -2.78056800 0.00000000
    Ir 0.00000000 0.00005600 0.00000000
    H -4.85221600 -3.62745600 0.00000000
    H -5.13574100 -1.20698000 0.00000000
    H -0.50258400 -3.18513500 0.00000000
    H -2.44301700 -4.64421900 0.00000000
    H -5.00021600 1.06382900 0.00000000
    H -4.67352300 3.67566300 0.00000000
    H -2.39890200 4.56043100 0.00000000
    H -0.37379900 2.90579800 0.00000000
    H -2.32971300 -1.77654500 0.00000000
    H -2.50697900 2.02787000 0.00000000
    H 1.57885000 -4.86192300 0.00000000
    H -0.84629400 -5.88507000 0.00000000
    H -2.74997000 -4.35772500 0.00000000
    H -2.80051900 4.43781300 0.00000000
    H -0.71552800 6.01603900 0.00000000
    H 1.52254200 5.05147800 0.00000000
    H 3.42159100 3.79819100 0.00000000
    H 5.51998600 2.20913700 0.00000000
    H 5.14873000 -0.20309400 0.00000000
    H 2.70313200 -1.12932200 0.00000000
    H 3.00995400 1.15712500 0.00000000
    H 5.24367900 0.20599300 0.00000000
    H 5.56755700 -2.38884300 0.00000000
    H 3.61296100 -3.84442200 0.00000000

    1 2 2.0 6 1.0 38 1.0
    2 3 1.0 39 1.0
    3 4 2.0 7 1.0
    4 5 1.0 13 3.0 37 1.0 46 1.0
    5 6 2.0 13 3.0 15 1.0 19 3.0 40 1.0
    6 13 1.0 19 3.0 41 1.0 50 1.0
    7 8 2.0 12 1.0
    8 9 1.0 42 1.0
    9 10 2.0 43 1.0
    10 11 1.0 14 3.0 20 3.0 44 1.0 51 1.0
    11 12 2.0 14 3.0 20 1.0 24 3.0 45 1.0
    12 14 1.0 37 1.0
    13 15 2.0 19 1.0 46 1.0
    14 20 2.0 24 1.0 47 1.0
    15 16 1.0 37 1.0
    16 17 2.0 25 1.0
    17 18 1.0 48 1.0
    18 19 2.0 49 1.0
    19 41 1.0 50 1.0
    20 21 1.0 44 1.0 51 1.0
    21 22 2.0 52 1.0
    22 23 1.0 53 1.0
    23 24 2.0 26 1.0
    24 37 1.0 45 1.0
    25 33 2.0 36 1.0
    26 27 2.0 31 1.0
    27 28 1.0 54 1.0
    28 29 2.0 55 1.0
    29 30 1.0 32 3.0 34 3.0 56 1.0 59 1.0
    30 31 2.0 32 3.0 33 3.0 34 1.0 57 1.0
    31 32 1.0 37 1.0
    32 33 1.0 34 2.0 58 1.0
    33 37 1.0 57 1.0
    34 35 1.0 56 1.0 59 1.0
    35 36 2.0 60 1.0
    36 61 1.0
    37
    38
    39
    40
    41 50 1.0
    42
    43
    44 51 1.0
    45
    46
    47
    48
    49
    50
    51
    52
    53
    54
    55
    56 59 1.0
    57
    58
    59
    60
    61

    H 0
    S 3 1.00
    19.2384000 0.0328280
    2.8987000 0.2312040
    0.6535000 0.8172260
    S 1 1.00
    0.1776000 1.0000000
    ****
    C 0
    S 7 1.00
    4233.0000000 0.0012200
    634.9000000 0.0093420
    146.1000000 0.0454520
    42.5000000 0.1546570
    14.1900000 0.3588660
    5.1480000 0.4386320
    1.9670000 0.1459180
    S 2 1.00
    5.1480000 -0.1683670
    0.4962000 1.0600910
    S 1 1.00
    0.1533000 1.0000000
    P 4 1.00
    18.1600000 0.0185390
    3.9860000 0.1154360
    1.1430000 0.3861880
    0.3594000 0.6401140
    P 1 1.00
    0.1146000 1.0000000
    ****
    N 0
    S 7 1.00
    5909.0000000 0.0011900
    887.5000000 0.0090990
    204.7000000 0.0441450
    59.8400000 0.1504640
    20.0000000 0.3567410
    7.1930000 0.4465330
    2.6860000 0.1456030
    S 2 1.00
    7.1930000 -0.1604050
    0.7000000 1.0582150
    S 1 1.00
    0.2133000 1.0000000
    P 4 1.00
    26.7900000 0.0182540
    5.9560000 0.1164610
    1.7070000 0.3901780
    0.5314000 0.6371020
    P 1 1.00
    0.1654000 1.0000000
    ****
    Ir 0
    S 3 1.00
    2.3500000 -1.6784642
    1.5820000 2.0952553
    0.5018000 0.4162934
    S 4 1.00
    2.3500000 1.6464467
    1.5820000 -2.2748150
    0.5018000 -1.0494357
    0.2500000 1.2167791
    S 1 1.00
    0.0598000 1.0000000
    P 3 1.00
    2.7920000 -0.3889212
    1.5410000 0.9077516
    0.5285000 0.4691443
    P 2 1.00
    0.5100000 -0.1170669
    0.0980000 1.0489002
    P 1 1.00
    0.0290000 1.0000000
    D 2 1.00
    1.2400000 0.5087022
    0.4647000 0.5862102
    D 1 1.00
    0.1529000 1.0000000
    ****
    ! Elements References
    ! ——– ———-
    ! Na – Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985).
    ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985).
    ! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985).
    !

    IR 0
    IR-ECP 4 60
    g potential
    5
    1 823.5880147 -0.1578014
    2 364.6613336 -1517.5270446
    2 55.7082801 -316.5306529
    2 12.0464544 -91.8880941
    2 3.5120610 -9.2241773
    s-g potential
    6
    0 188.0490770 3.1578014
    1 340.4194712 26.8322577
    2 128.2373673 800.4250007
    2 33.8644961 369.4050683
    2 4.7560005 242.4171899
    2 3.9649974 -118.2173282
    p-g potential
    5
    0 289.7291139 2.1578014
    1 87.4633789 61.9678610
    2 30.4363766 269.0581986
    2 4.0553412 231.1654793
    2 3.5525341 -133.6952667
    d-g potential
    5
    0 136.4017106 3.1578014
    1 95.0776925 45.9349803
    2 49.2258410 359.0344668
    2 15.0874145 176.4740119
    2 4.0405764 54.5155286
    f-g potential
    5
    0 127.3507908 3.9546197
    1 66.2364374 52.9773655
    2 34.4299229 274.8643383
    2 10.1995721 137.2047338
    2 2.5409702 14.8633305

    Ir 0.82

    ————————————-
    and this is the output with error 2070:

    Entering Link 1 = C:\G03W\l1.exe PID= 3580.

    Copyright (c) 1988,1990,1992,1993,1995,1998,2003, Gaussian, Inc.
    All Rights Reserved.

    This is the Gaussian(R) 03 program. It is based on the
    the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.),
    the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.),
    the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.),
    the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.),
    the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.),
    the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon
    University), and the Gaussian 82(TM) system (copyright 1983,
    Carnegie Mellon University). Gaussian is a federally registered
    trademark of Gaussian, Inc.

    This software contains proprietary and confidential information,
    including trade secrets, belonging to Gaussian, Inc.

    This software is provided under written license and may be
    used, copied, transmitted, or stored only in accord with that
    written license.

    The following legend is applicable only to US Government
    contracts under DFARS:

    RESTRICTED RIGHTS LEGEND

    Use, duplication or disclosure by the US Government is subject
    to restrictions as set forth in subparagraph (c)(1)(ii) of the
    Rights in Technical Data and Computer Software clause at DFARS
    252.227-7013.

    Gaussian, Inc.
    Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA

    The following legend is applicable only to US Government
    contracts under FAR:

    RESTRICTED RIGHTS LEGEND

    Use, reproduction and disclosure by the US Government is subject
    to restrictions as set forth in subparagraph (c) of the
    Commercial Computer Software – Restricted Rights clause at FAR
    52.227-19.

    Gaussian, Inc.
    Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA

    —————————————————————
    Warning — This program may not be used in any manner that
    competes with the business of Gaussian, Inc. or will provide
    assistance to any competitor of Gaussian, Inc. The licensee
    of this program is prohibited from giving any competitor of
    Gaussian, Inc. access to this program. By using this program,
    the user acknowledges that Gaussian, Inc. is engaged in the
    business of creating and licensing software in the field of
    computational chemistry and represents and warrants to the
    licensee that it is not a competitor of Gaussian, Inc. and that
    it will not use this program in any manner prohibited above.
    —————————————————————

    Cite this work as:
    Gaussian 03, Revision B.01,
    M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria,
    M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven,
    K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi,
    V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega,
    G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota,
    R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao,
    H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross,
    C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev,
    A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala,
    K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg,
    V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain,
    O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari,
    J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford,
    J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz,
    I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham,
    C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill,
    B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople,
    Gaussian, Inc., Pittsburgh PA, 2003.

    *********************************************
    Gaussian 03: x86-Win32-G03RevB.01 3-Mar-2003
    31-Dec-2011
    *********************************************
    %chk=C:\Users\Enrico D\Desktop\Ir(ppy)3 testgrd.chk
    Default route: MaxDisk=4gb
    ———————————————————————-
    # opt freq td rb3lyp/gen geom=connectivity int=ultrafine pop=(readradi
    i,mk) pseudo=read
    ———————————————————————-

    Warning: this job cannot use analytic gradients
    and so will do many energy evaluations.

    1/14=-1,26=3,29=20000,38=1,57=2/1,14;
    2/17=6,18=5,29=3,40=1/2;
    3/5=7,11=2,16=1,17=8,25=1,30=1,74=-5,75=5/1,2,8,3;
    4/7=1/1;
    5/5=2,38=5/2;
    8/6=1,10=1,27=536870912/1;
    9/27=536870912,42=1/14;
    6/7=2,8=2,9=2,10=2,15=8,20=101/1,2;
    1/14=-1/14(1);
    99//99;
    2/29=3/2;
    3/5=7,6=1,11=2,16=1,17=8,25=1,30=1,74=-5,75=5,82=7/1,2,8,3;
    4/5=5,7=1,16=3/1;
    5/5=2,38=5/2;
    8/6=1,10=1,27=536870912/1;
    9/27=536870912,42=1,49=4/14;
    1/14=-1/14(-6);
    2/29=3/2;
    6/7=2,8=2,9=2,10=2,15=8,20=101/1,2;
    99//99;
    ——————-
    Title Card Required
    ——————-
    Symbolic Z-matrix:
    Charge = 0 Multiplicity = 1
    C -3.99749 -2.9838 0.
    C -4.15709 -1.63959 0.
    C -2.90823 -0.74768 0.
    C -1.67055 -1.23449 0.
    C -1.48668 -2.76506 0.
    C -2.57441 -3.5823 0.
    C -2.91748 0.72025 0.
    C -4.02165 1.49665 0.
    C -3.83064 3.01655 0.
    C -2.56851 3.50396 0.
    C -1.37319 2.5236 0.
    N -1.57202 1.23716 0.
    C -1.49898 -2.45092 0.
    C -1.65119 2.67013 0.
    N -0.28545 -1.97987 0.
    C 0.83493 -2.88661 0.
    C 0.71469 -4.23096 0.
    C -0.69702 -4.82555 0.
    C -1.75026 -3.97629 0.
    C -1.81515 4.02072 0.
    C -0.58536 4.954 0.
    C 0.65863 4.42016 0.
    C 0.80667 2.89257 0.
    C -0.23377 2.06411 0.
    C 2.10159 -2.14478 0.
    C 2.08254 2.16648 0.
    C 3.30703 2.73435 0.
    C 4.52771 1.80883 0.
    C 4.31866 0.47211 0.
    C 2.87195 -0.07273 0.
    N 1.85736 0.74281 0.
    C 3.13809 0.09483 0.
    C 1.90442 -0.82953 0.
    C 4.38968 -0.43868 0.
    C 4.5828 -1.97037 0.
    C 3.49839 -2.78057 0.
    Ir 0. 0.00006 0.
    H -4.85222 -3.62746 0.
    H -5.13574 -1.20698 0.
    H -0.50258 -3.18514 0.
    H -2.44302 -4.64422 0.
    H -5.00022 1.06383 0.
    H -4.67352 3.67566 0.
    H -2.3989 4.56043 0.
    H -0.3738 2.9058 0.
    H -2.32971 -1.77655 0.
    H -2.50698 2.02787 0.
    H 1.57885 -4.86192 0.
    H -0.84629 -5.88507 0.
    H -2.74997 -4.35773 0.
    H -2.80052 4.43781 0.
    H -0.71553 6.01604 0.
    H 1.52254 5.05148 0.
    H 3.42159 3.79819 0.
    H 5.51999 2.20914 0.
    H 5.14873 -0.20309 0.
    H 2.70313 -1.12932 0.
    H 3.00995 1.15713 0.
    H 5.24368 0.20599 0.
    H 5.56756 -2.38884 0.
    H 3.61296 -3.84442 0.

    NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-
    NUMERICAL EIGENVECTOR FOLLOWING MINIMUM SEARCH
    INITIALIZATION PASS

    ************************************************
    ** ERROR IN INITNF. NUMBER OF VARIABLES ( 0) **
    ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) **
    ************************************************

    Error termination via Lnk1e in C:\G03W\l114.exe at Sat Dec 31 14:28:19 2011.
    Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds.
    File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 1 Scr= 1

    …………………

    for simplest calculations or for smallest molecules there is no problem.But for biggest ones…
    WHAT SHOULD I DO?
    IN GENERAL, CAN YOU HELP ME TO SET UP TDDFT CALCULATIONS for excited states FOR TRANSITION METALS SUCH AS Ru and Ir, what are the best settings and the corrects one?
    There are errors in the input file? (Syntax, Keywords…?)…
    this is the molecule: http://www.lookchem.com/300w/2010/0714/94928-86-6.jpg
    i use:
    GaussView 5.0
    Gaussian03
    ChemBio Office for structure designing

    Many thanks.
    Best Regards,

    Enrico D’Ortenzio
    Oricola (Italy)
    University of Tor Vergata, Rome

    Reply
    • Nicola | January 13, 2012 at 4:58 AM

      Hi, I make TD-DFT with metal complex and I usually use the lanl2dz basis set with the cam-B3LYP functional for TD calculation and they give good result compared with experimental data. I suggest you to include also the solvent effect with PCM because the effect of solvent in the optimization steps and solvatochromism is important.
      But it’s better that you first optimize the structure and after run TD job.
      Try this for the optimization:

      #p opt=tight b3lyp/lanl2dz scrf=(solvent=water) geom=connectivity pop=full

      and this for TD:

      #p cam-b3lyp/LANL2DZ nosym scf=maxcyc=2048 TD=NStates=35 IOP(9/40=2) IOp(8/11=1) scrf=(solvent=water)

      (I used water as solvent but you can change it, the same for the number of excited state you need)
      I hope this help
      Please let me know if this work
      Nicola

      Reply
  30. Mariana | January 6, 2012 at 2:53 PM

    Estimado Dr. Estoy estudiando una reacción química (Diels-Alder) y quisiera los coeficientes de cada átomo en el HOMO y el LUMOm cómo puedo hacerlo? Aun estoy entendiendo este programa, gracias.

    Reply
  31. mohamad | January 7, 2012 at 10:58 AM

    Dear Dr. Barroso

    thanks a lot for your helpful posts.
    I want to calculate overlap population analysis in G03.
    please help me.
    Best regards.

    Reply
  32. Gürkan KESAN | January 10, 2012 at 10:11 AM

    Dear Dr. Joagguin,

    I am PhD student and studying with Gaussian for biological and argonometalic molecules or complexes. Can you give me some information about TDDFT calculation and Infrared-Raman calculations for this exiated state(s)? I examine some fields and help field for gaussian but I have some question… And also may you tell me system rational for gaussian?

    Thank you very much, in advance…

    Reply
  33. Enrico D. | January 17, 2012 at 3:01 PM

    hello ,
    i do tddft uv-vis spectra of Ni(CH2S2)2, for more excited states..with g09w
    but..
    for some calculations i used to specify pseudopotentials with geneecp keyword to indicate the lanld2z pseudopotential for nickel…and 6-311g(3d,2p) for C,S,H
    at higher frequencies, between 200-300 nm, using 6-311g for all atoms or specifying lanl2dz for Ni, i notice a split in one of the peak (the one at 270nm), i.e. the peak is split into two different peaks.
    in the experimental spectrum this peak is at ca. 300nm and there is no splitting!…
    what is the explanation of this effects? what are the problems related to higher frequencies states?can it depend that this is a Nickel compound? in what way it can depend by calculations?:

    i do tddft calculations using b3lyp/6-311G(3d,2p), PCM for solvent(hexane)
    or b3lyp/geneecp specifying lanld2z for Ni at the end of the input after the coordinates.

    MANY THANKS
    Enrico D.

    Reply
  34. Enrico | January 18, 2012 at 6:31 AM

    Hi there,
    i use lsda functional in my calculations on Ni, and i would use pure lda functional to compare results with lsda calculations, to understand how the spin affects (and if) the measurement.
    HOW TO SET PURE LDA CALCULATION IN G09W?, since there is no pure lda in gaussview?

    Best regards,
    Enrico

    Reply
  35. vasanth.v | February 3, 2012 at 11:45 PM

    respected sir
    i am working with go3 as part of my research work. As part of my study i need to calculate Hyperpolarizability of molecule. For this, i used syntax

    #p polar scf = maxcycles=500 freq = noraman b3lyp/6-311+g

    finally it is giving only polar and dipolar values, but not hyperpolar.
    kindly help me in this regard

    thank you very much in advance

    vasanth

    Reply
  36. Bijan Mondal | February 6, 2012 at 8:40 AM

    Respected Sir,
    I have done NBO calculation on diborane using standard basis set and DFT method in order to visualize the 3-centered bonds. But the NBO number appears involving 3-center bond(e.g, 1 & 4) is not matching whenever I am visualizing in gauss view rather its sum other number MO.
    Kindly halp me in this regards.

    Best regards,
    Bijan

    Reply
  37. jyotsna arora | February 11, 2012 at 7:34 AM

    Dear Sir,

    i am trying to do DFT calculation of TiO2 crystal for interaction qith simple molecules like water
    But in doing so using G09 (w) when I’m taking / cleaving the crystal from a particular surface like 0 0 1 surface and interacting the water molecule

    the error is

    “Symmetry turned off by external request
    Symmetry turned off
    Cannot cope with the ghost atoms or with translational vectors”

    Do I have to give a PBC calculation for the crystal
    Also how do I see the interacting atoms as it is a symmetrical structure and on cleaving the infinte structure still remains

    Do I have to saturate the O ends of TiO2 with hydrogen/ make it a double bond?

    Regards
    Jyotsna

    Reply
  38. Bijan Mondal | February 13, 2012 at 12:32 AM

    Dear Sir,
    I have a quarry..
    Can we do Fukui index calculation using gaussian 09 or 03?

    Reply
    • joaquinbarroso | February 16, 2012 at 11:48 PM

      Yes, Bijan. Gaussian can calculate Fukui indexes. Look in this blog for a post called “How to calculate Fukui Indexes” it will give you a step by step procedure on the subject.

      I hope this helps

      Reply
  39. Rajesh | February 14, 2012 at 1:44 PM

    Hi

    Can you pls help me to understand how these lone pair represntaion from NBO analysis means?

    57. (0.22868) LP*( 6)Ru 11 s( 42.76%)p 1.32( 56.57%)d 0.01( 0.64%)
    f 0.00( 0.03%)g 0.00( 0.00%)
    0.0000 0.6536 -0.0100 -0.0140 0.0085
    0.0009 0.0000 -0.0561 0.0109 -0.0053
    0.0000 -0.7439 -0.0007 0.0019 0.0000
    -0.0939 0.0024 -0.0108 0.0096 -0.0268
    -0.0119 -0.0371 -0.0078 0.0078 0.0319
    -0.0045 -0.0071 -0.0445 0.0216 -0.0102
    0.0075 -0.0104 -0.0123 0.0047 0.0008
    0.0039 -0.0028 -0.0023 0.0018 0.0017
    -0.0048 0.0030 0.0013 0.0057 -0.0057
    0.0101 0.0043 0.0006 -0.0004 0.0004
    -0.0013 -0.0002 -0.0012 -0.0001 -0.0023
    -0.0006
    My question

    How it is a kind of sp hybrid. I beleive usually the lone pairs are non bonding oribatals..If am wrong pls correct me..

    Thanks
    Rajesh

    Reply
    • joaquinbarroso | February 16, 2012 at 11:42 PM

      Hello Rajesh!

      Lone pairs are indeed non bonding orbitals, but they can be hybridized. Think about ammonia NH3 for instance, the valence orbitals of the Nitrogen atom are sp3 hybridized, this includes all three N-H bonds but also includes the lone pair on the N atom.
      Please search for my post on Pauling’s model of hybridized orbitals in this same blog. Also you could take a look at Gillespie’s VSEPR theory (well, more like a model), you’ll realize that lone pairs get hybridized too.

      I hope this helps! Have a nice day

      Reply
  40. Moshe Nathan | February 14, 2012 at 7:19 PM

    Dear Dr Barroso,
    I am having trouble with molekel while analyzing a pdb file I created. The file was originally created as a trajectory / trr file by gromacs. I converted it to a pdb. I have done this dozens of times in the past. When analyzing the video in molekel, the carboxyl terminal end of the dipeptide seems to detach, specifically the carbon attached to the hydrogen. I reran this simulation many times and it is always the same way. I even ran a different dipeptide and again the same thing happened. Interesting to note, if there is a carboxyl group in the side chain of the dipeptide, the issue does not arise, only for the terminal end. I can included the pdb as an attachment in an email, so it can be examined. Any assistance with this matter would be appreciated.

    Moshe Nathan

    Brooklyn College – Dept. of Chemistry

    Brooklyn, NY

    Reply
    • joaquinbarroso | February 16, 2012 at 11:27 PM

      Hi Moshe

      What version of Molekel are you using? If I remember correctly, in Molekel4.x you have to go to the main interface and click on the ‘bond attributes’ button, then on ‘add bond’ and select the atoms you want to be bonded. After that you have to right-click on the main screen and then go to ‘done picking’. Well, this last bit is only if you don’t have them bonded from the start, which I think is not your case but bear with me.
      On the animate/play window there are a couple of useful options “keep bonds” and “superimpose”. The first one will continue to draw all bonds throughout the movie regardless of the bond distance (which is the only criteria molekel is concerned whith when painting bonds between atoms). The second one will re-orient the molecule (or the coordinate system) to make a fluid movie. Sometimes the molecule gets re-oriented for convenience during the optimization process, depending on the case and the software used.
      I hope this helps, Moshe. I hope I get to know the Brooklyn College one of these days

      Best wishes

      Reply
  41. Erik | February 15, 2012 at 2:58 PM

    Buen día!

    Le escribo porque tengo un problema en los inputs para G09 empleando oniom y derivados del cis-platino, para la capa baja utilizo un semiempírico (PM3) y para la alta pretendo utilizar pseudopotenciales, pero al especificar la base de pseudopotenciales (SDD) no se en que parte del input esté mi error, pero no me reconoce solo para Pt dicha base. el input es el siguiente:

    %chk=oniom1
    %mem=512MB
    %nproc=8
    # opt=Maxcycle=1024 oniom(pbepbe/GenECP:PM6) scf=qc geom=connectivity pseudo=Read

    oniom1

    0 1 0 1 0 1
    especificaciones de la molécula

    C H O N Cl 0
    6-31G(d,p)
    Pt 0
    S 3 1.00
    2.5470000 -1.4739175
    1.6140000 1.9115719
    0.5167000 0.3922319
    S 4 1.00
    2.5470000 1.4388166
    1.6140000 -2.0911821
    0.5167000 -1.0921315
    0.2651000 1.3426596
    S 1 1.00
    0.0580000 1.0000000
    P 3 1.00
    2.9110000 -0.5247438
    1.8360000 0.9671884
    0.5982000 0.5438632
    P 2 1.00
    0.6048000 -0.1061438
    0.0996000 1.0383102
    P 1 1.00
    0.0290000 1.0000000
    D 2 1.00
    1.2430000 0.5598150
    0.4271000 0.5511090
    D 1 1.00
    0.1370000 1.0000000

    Gracias de antemano.

    Erik Díaz
    Departamento de química
    Universidad de Guanajuato

    Reply
    • joaquinbarroso | February 16, 2012 at 11:17 PM

      Hola Erik!

      Bien, pues no veo donde está el pseudopotencial. Solo veo las bases. Intenta utilizar Gen en lugar de GenECP pues tal vez esté interfiriendo con la instrucción pseudo=read pero insisto en que no veo en ningún lado el ECP, el cual lo puedes bajar de la EMSL basis set exchage site (búscalo así en google)

      Saludos y ojalá nos veamos por Guanajuato un día de estos.

      Reply
  42. sridesikan | February 17, 2012 at 12:06 AM

    Dear Joaquin

    Can you say the difference between binding energy and interaction energy when we handle the biomolecular system. Thank you.

    Regards,
    Desikan.

    Reply
  43. Rajesh | February 19, 2012 at 3:05 AM

    Hi,

    Recently I have perfomed a NBO analyis on metal-alkene complex. I have found that the stablization energy (E2) given by the second order pertubation analysis on donor-acceptor interactions is very high (ranging from 30-50 kcal/mol different alkene complexes). .I don’t think I can take this value in a quantitave manner). The total binding energy for those metal-alekene complexes are ranges from 15-21 kcal/mol..Can u pls explain to me this discrepancies in these values?

    Reply
  44. vasanth.v | February 24, 2012 at 12:21 AM

    respected sir
    i want to study the solvent effects on my molecule. For this i used syntax

    #t scf=maxcycles=1000 b3lyp/6-311+g scrf=(cpcm,solvent=nitromethane,read) freq=raman

    but 1301.exe is stopped working message is being displayed after few seconds?

    pl help in this regard

    Reply

Leave a Reply

Fill in your details below or click an icon to log in:

Gravatar
WordPress.com Logo

You are commenting using your WordPress.com account. ( Log Out / Change )

Twitter picture

You are commenting using your Twitter account. ( Log Out / Change )

Facebook photo

You are commenting using your Facebook account. ( Log Out / Change )

Cancel

Connecting to %s

Follow

Get every new post delivered to your Inbox.

Join 176 other followers